Two senators who oversee the budget of the National Weather Service have said they will not give the department permission to repurpose $35.5 million until they know why officials have “manipulated” their budget.

The reprimand came in response to a request from the Weather Service last week to reallocate money from one department budget to another for the rest of the fiscal year to avoid furloughs. An internal investigation concluded that for several years, the department had carried out this practice informally without asking Congress, misdirecting millions of dollars approved for various functions and reallocating the money to 122 weather offices around the country.

The investigation prompted the abrupt retirement Friday of the Weather Service’s director, John L. “Jack” Hayes, after the replacement of the agency’s chief financial officer.

In a letter the same day to Commerce Secretary John Bryson, Sens. Barbara A. Mikulski (D-Md.) and Kay Bailey Hutchison (R-Tex.), chairman and ranking minority member, respectively, of the Senate Appropriations subcommittee on commerce, justice, science and related agencies, questioned whether the department covered a failure to properly estimate its budget for local forecast offices by siphoning money allocated for equipment and technology upgrades.

“It appears that this practice may have become a recurring pattern over the years at NWS, which has left the committee and the Congress in the dark about the true needs and expenditures of the [department] and the movement of appropriated funds,” the senators wrote.

The request “raises more questions than it answers,” they said.

The “committee has been misled about how appropriated funds and approved spending plans have been manipulated,” the senators wrote in the letter.

Allowing the process to continue with a green light from Congress would only “continue the self-cannibalization funding model,” they wrote.

Bryson oversees the Weather Service through the National Oceanic and Atmospheric Administration. NOAA officials declined to comment Tuesday.

NOAA officials have said there is no evidence of fraud or personal gain from the misdirected money. But the investigation, prompted by anonymous complaints in 2010 and 2011, concluded that senior Weather Service staff operated “outside the bounds of acceptable financial management.”

Richard J. Hirn, general counsel for the National Weather Service Employees Organization, said NOAA has long been aware of a structural deficit within the Weather Service but failed to address it.

“NOAA has known for years that the [Weather Service] has been underfunded and cannot make ends meet,” he said. The union lobbied NOAA to make covering the deficit its top priority, but “it did not happen,” he said.

The Weather Service found itself without funding for critical forecast operations, he said.

If Congress does not formally allow the shortfall to be covered, “we have been told that forecasters will soon be furloughed nationwide — this, during the height of severe weather and hurricane season,” Hirn said.