WASHINGTON — Justice Department watchdogs ran into an unexpected roadblock last year when they began examining the role of federal drug agents in the fatal shootings of unarmed civilians during raids in Honduras.
The Drug Enforcement Administration balked at turning over emails from senior officials tied to the raids, according to the department’s inspector general. It took nearly a year of wrangling before the D.E.A. was willing to turn over all its records in a case that the inspector general said raised “serious questions” about agents’ use of deadly force.
The continuing Honduran inquiry is one of at least 20 investigations across the government that have been slowed, stymied or sometimes closed because of a long-simmering dispute between the Obama administration and its own watchdogs over the shrinking access of inspectors general to confidential records, according to records and interviews.
The impasse has hampered investigations into an array of programs and abuse reports — from allegations of sexual assaults in the Peace Corps to the F.B.I.’s terrorism powers, officials said. And it has threatened to roll back more than three decades of policy giving the watchdogs unfettered access to “all records” in their investigations.
“The bottom line is that we’re no longer independent,” Michael E. Horowitz, the Justice Department inspector general, said in an interview.
The restrictions reflect a broader effort by the Obama administration to prevent unauthorized disclosures of sensitive information — at the expense, some watchdogs insist, of government oversight.
Justice Department lawyers concluded in a legal opinion this summer that some protected records, like grand jury transcripts, wiretap intercepts and financial credit reports, could be kept off limits to government investigators. The administration insists there is no intention of curtailing investigations, but both Democrats and Republicans in Congress have expressed alarm and are promising to restore full access to the watchdogs.
The new restrictions grew out of a five-year-old dispute within the Justice Department. After a series of scathing reports by Glenn Fine, then the Justice Department inspector general, on F.B.I. abuses in counterterrorism programs, F.B.I. lawyers began asserting in 2010 that he could no longer have access to certain confidential records because they were legally protected.
That led to a series of high-level Justice Department reviews, a new procedure for reviewing records requests and, ultimately, a formal opinion in July from the department’s Office of Legal Counsel. That opinion, which applies to federal agencies across the government, concluded that the 1978 law giving an inspector general access to “all records” in investigations did not necessarily mean all records when it came to material like wiretap intercepts and grand jury reports.
The inspector-general system was created in 1978 in the wake of Watergate as an independent check on government abuse, and it has grown to include watchdogs at 72 federal agencies. Their investigations have produced thousands of often searing public reports on everything from secret terrorism programs and disaster responses to boondoggles like a lavish government conference in Las Vegas in 2010 that featured a clown and a mind reader.
Not surprisingly, tensions are common between the watchdogs and the officials they investigate. President Ronald Reagan, in fact, fired 15 inspectors general in 1981. But a number of scholars and investigators said the restrictions imposed by the Obama administration reflect a new level of acrimony.
“This is by far the most aggressive assault on the inspector general concept since the beginning,” said Paul Light, a New York University professor who has studied the system. “It’s the complete evisceration of the concept. You might as well fold them down. They’ve become defanged.”
While President Obama has boasted of running “the most transparent administration in history,” some watchdogs say the clampdown has scaled back scrutiny of government programs.
“This runs against transparency,” said the Peace Corps inspector general, Kathy Buller.
At the Peace Corps, her office began running into problems two years ago in an investigation into the agency’s handling of allegations of sexual assaults against overseas volunteers. Congress mandated a review after a volunteer in Benin was murdered in 2009; several dozen volunteers reported that the Peace Corps ignored or mishandled sexual abuse claims.
But Peace Corps lawyers initially refused to turn over abuse reports, citing privacy restrictions. Even after reaching an agreement opening up some material, Ms. Buller said investigators have been able to get records that are heavily redacted.
“It’s been incredibly frustrating,” she said. “We have spent so much time and energy arguing with the agency over this issue.”
The Peace Corps said in a statement, however, that it was committed to “rigorous oversight” and has cooperated fully with the inspector general.
Agencies facing investigations are now sometimes relying on the Justice Department’s opinion as justification for denying records — even records that are not specifically covered in the opinion, officials said.
At the Commerce Department, the inspector general this year shut down an internal audit of enforcement of international trade agreements because the department’s lawyers, citing the Justice Department’s guidance, refused to turn over business records that they said were “proprietary” and protected.
The Environmental Protection Agency’s inspector general has reported a series of struggles with the organization over its access to documents, including records the agency said were classified or covered by attorney-client privilege. And investigators at the Postal Service, a special Afghanistan reconstruction board, and other federal agencies have complained of tightened restrictions on investigative records as well.
Hopes of a quick end to the impasse have dimmed in recent days after the Obama administration volunteered to restore full access for the Justice Department’s inspector general — but not the other 71 watchdogs.
Attorney General Loretta E. Lynch, asked about the issue at a House hearing last week, said the proposal was intended to ensure, at least at the Justice Department, “that the inspector general would receive all the information he needed.”
But watchdogs outside the Justice Department said they would be left dependent on the whims of agency officials in their investigations.
“It’s no fix at all,” said Senator Charles E. Grassley, Republican of Iowa, who leads the Judiciary Committee.
In a rare show of bipartisanship, the administration has drawn scorn from Democrats and Republicans. The Obama administration’s stance has “blocked what was once a free flow of information” to the watchdogs, Senator Patrick J. Leahy of Vermont, the ranking Democrat on the Judiciary Committee, said at a hearing.
A Justice Department spokeswoman, Emily Pierce, said in a statement on Friday: “Justice Department leadership has issued policy guidance to ensure that our inspector general gets the documents he requests as quickly as possible, even when those documents are protected by other statutes protecting sensitive information. The department is unaware of any instance in which the inspector general has sought access to documents or information protected from disclosure by statute and did not receive them.”
Nowhere has the fallout over the dispute been felt more acutely than at the Justice Department, where the inspector general’s office said 14 investigations had been hindered by the restricted access.
These include investigations into the F.B.I.’s use of phone records collected by the National Security Agency, the government’s sharing of intelligence information before the 2013 Boston Marathon bombings, a notorious gun-tracing operation known as “Fast and Furious” and the deadly Honduran drug raids.
In the case of the Honduran raids, the inspector general has been trying to piece together the exact role of D.E.A. agents in participating in, or even leading, a series of controversial drug raids there beginning in 2011.
Details of what happened remain sketchy even today, but drug agents in a helicopter in 2012 reportedly killed four unarmed villagers in a boat, including a pregnant woman and a 14-year-old boy, during a raid on suspected drug smugglers in northeastern Honduras. They also shot down several private planes — suspected of carrying drugs — in possible violation of international law.
An investigation by the Honduran government cleared American agents of responsibility. But when the inspector general began examining the case last year, D.E.A. officials refused to turn over emails on the episodes from senior executives, the inspector general’s office said. Only after more than 11 months of back-and-forth negotiations were all the records turned over.
The D.E.A. refused to comment on the case, citing the investigation. A senior Justice Department official, speaking on the condition of anonymity because of the continuing review, said the refusal to turn over the records was the flawed result of “a culture within the D.E.A.” at the time — and not the result of the Justice Department’s new legal restrictions.
Mr. Horowitz, the inspector general, said the long delay was a significant setback to his investigation. He now hopes to complete the Honduran review early next year.
In the meantime, the watchdogs say they are looking to Congress to intervene in a dispute with the administration that has become increasingly messy.
“It’s essential to enshrine in the law that the inspector general has access to all agency records,” said Mr. Fine, who is now the Pentagon’s principal deputy inspector general. “The underlying principle is key: To be an effective inspector general, you need the right to receive timely access to all agency records.”
Investigations are being hampered by a dispute between the White House and its own watchdogs over the shrinking access of inspectors general to confidential files.