The director of the National Weather Service has retired after an investigative report found senior staff members at the agency had misdirected millions of dollars and operated “outside the bounds of acceptable financial management.”

John L. “Jack” Hayes, assistant administrator of the National Oceanic and Atmospheric Administration and NWS director since 2007, retired Friday. That was the day after a departmental investigation said that for several years, the NWS has taken money Congress had provided for certain functions and reallocated the money to 122 weather offices around the country.

“The fact that the team did not find any evidence of fraud or personally [sic] financial gain does not lessen the severity of the misconduct,” said a memorandum from Deputy Commerce Secretary Rebecca M. Blank.

The NWS chief financial officer was replaced last year and the department began investigating anonymous complaints about the misallocation of funds in 2010 and 2011.

Senate Commerce, Science and Transportation Committee member Olympia J. Snowe (R-Maine) called the reports “deeply troubling.”

John L. “Jack” Hayes was National Weather Service director since 2007. He did not mention the investigative report in a farewell he wrote to employees on Friday. (Benjamin C Tankersley/For the Washington Post)

“I am further alarmed that the investigative report raises fundamental concerns that the core operations of the National Weather Service are underfunded, and that the current process in the Department of Commerce is broken, as it ‘did not encourage questioning or provide independent channels for reporting dubious budget decisions,’ ” Snowe, ranking member of the Oceans, Atmosphere, Fisheries and Coast Guard subcommittee, said in a statement.

Hayes’s retirement, first reported by MSNBC, came in the last paragraph of a news release Friday announcing that Laura Furgione would take over NWS on an acting basis.

Hayes is a longtime NOAA official, a former Air Force colonel and often the NWS’s public face in times of extreme weather events. He did not mention the investigative report in a farewell he wrote to employees.

“It’s been a great honor to serve with the men and women of the National Weather Service, but now it is time for me to move to the next chapter of my life and make room for the next generation of leaders,” Hayes wrote. “Your successes are too numerous to count — most memorably, your victory in the ‘Super Bowl’ of extreme weather years in 2011, when you saved countless lives with advance warnings for Hurricane Irene, the Joplin tornado, the Alabama tornadoes, and historic floods.”

Scott Smullen, NOAA communications and external affairs deputy director, acknowledged in a statement that NWS “engaged in the reprogramming of funds without Congressional notification as required by the applicable Federal Appropriations Acts.”

But, he added: “The investigation also found that no funds were used on inappropriate items, they were simply used in different categories than originally budgeted. The investigation found no evidence of corruption or personal financial gain in these actions. We do not believe any money was moved out of the National Weather Service.”

Richard Hirn, general counsel and legislative director for the National Weather Service Employees Organization, said as much as $30 million a year has been “reprogrammed” in the past to avoid furloughs and layoffs in weather stations.

“Robbing Peter to pay Paul is what has been going on,” he said.

He said the NWS is asking Congress for permission to repurpose $28 million for the rest of the fiscal year to avoid furloughs.

In other bad news for NOAA, a report from the Commerce Department’s inspector general said the agency did not provide proper justification in handing out $43.8 million in performance awards to private contractors.

“On some contracts, the performance monitors did not maintain documentation to support the ratings,” the report said, “and on other contracts, the examples and comments provided did not contain enough information to determine whether the ratings, award fees and award terms were warranted.”

Jason Samenow contributed to this report.