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.