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 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. 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. The bottom line is that we're no longer independent," Michael E. Horowitz, the Justice Department inspector general, said. 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. Tensions are common between the watchdogs and the officials they investigate. But ... 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.