Michael G. Carroll, the deputy inspector general for the U.S. Agency for International Development, will retire at the end of the year after allegations by whistleblowers that his office improperly altered and removed negative findings from audit reports before releasing them to the public.

Carroll, 60, said his decision to retire after 32 years with the federal government — the last three as acting inspector general — has nothing to do with the whistleblowers’ allegations. He said he hopes the White House will quickly name a replacement to run the office, which examines billions of dollars in spending by USAID around the world.

“I am extremely proud to have served with such dedicated colleagues and I will look back fondly on the many wonderful friendships we have had,” Carroll said in an e-mail to his staff Friday. “I hope that our focus on improving the organizational culture continues to bear fruit and that it creates a solid foundation for the future.”

He said Deputy Inspector General Catherine Trujillo will take over the day-to-day operations of the office until a permanent replacement is named. He did not say what he plans to do after stepping down.

“It has been an honor to lead this great organization for the past three years and I wish everyone the best,” Carroll said.

In October, The Washington Post reported that eight current and former auditors and employees at the USAID inspector general’s office complained that negative findings had been stricken from audit reports between 2011 and 2013. The Post also found that sharply critical passages had been removed from a dozen audits and that more than 400 negative comments about USAID and its mission offices had been deleted from final reports.

The Post also reported that Sen. Tom Coburn (R-Okla.) and investigators working for the Senate Homeland Security and Governmental Affairs Committee had been examining the allegations and interviewing whistleblowers.

Auditors and others in the inspector general’s office said Carroll had increasingly become a defender of USAID and he did not want to create controversy while awaiting Senate confirmation to become the permanent inspector general. Carroll and his deputies have denied the accusations.

The inspector general’s office said the alterations and deletions were based on editorial judgments and accounting principles. Deputies in the office said there was no effort to play down reports that cast USAID or any other federal agency in a negative light. The deputies also said that the office has changed its auditing policies and has become more transparent by posting once- confidential audit information on its Web site.

As The Post was preparing to publish its examination of the whistleblowers’ allegations, Carroll on Oct. 22 withdrew his nomination to become the permanent inspector general. He noted that he did not expect the Senate to approve his nomination in the near future but he said he planned to remain in the office as a deputy inspector general.

Carroll did not say why he changed his mind. In a brief e-mail exchange with The Post on Monday, he said that his e-mail to his staff “captures my sentiments completely, so I’m not certain there is anything more that needs to be said.”

When asked if the allegations by the whistleblowers factored into his decision, Carroll said, “Not at all.”