The Reagan administration is proposing that five federally chartered credit agencies pay a user fee to the U.S. Treasury when they issue bonds, a change in policy that could raise interest rates on student loans, federal farm loans and home mortgages.

If approved by Congress, the proposal would add less than 1/10 of 1 percent to interest rates charged by the Federal Home Loan Mortgage Corp., the Federal National Mortgage Association, the Federal Home Loan Bank Board, the Student Loan Marketing Association and the Farm Credit Administration.

All five were chartered by the federal government to raise money in the private credit market to buy mortgage loans, student loans or farm loans, thereby increasing the flow of capital to those industries.

The Bank Board and Farm Credit Administration remain part of the federal government, but the other three organizations are to one degree or another owned by stockholders. But all five are able to borrow at lower rates because their ties to the federal government are seen as a tacit government guarantee of their debts.

Lobbyists for the housing industry, student loan associations and farmers all protested the proposal yesterday, saying the fees would be passed on to individual borrowers and the proposal would undermine federal initiatives to provide home, education and farm credit.

Industry officials also questioned the administration's motives, saying that the proposal would effectively make the securities issued by the agencies less attractive to investors, possibly increasing the relative attractiveness of Treasury bonds.

The proposal by the Office of Management and Budget is to charge a user fee of 0.05 percent on all new forms of borrowing by the agencies starting in fiscal year 1986, which begins next Oct. l. The user fee for debt issues -- but not mortgage-backed securities -- would increase to 0.083 percent in fiscal year 1987.

"Given that these government-sponsored agencies have a market advantage arising from their ties to the federal government, and given that there is no viable proposal to eliminate those ties, we've decided to charge for them," said J. Gregory Ballentine, OMB's associate director for economic policy.

OMB estimated the total outstanding debt for all five agencies for the end of 1984 at $325 billion. It said it expects the proposal to raise an estimated $100 million in revenue for the Treasury Department in the next two or three years, accumulating to $500 million total by the end of the decade. Ballentine said the proposal would be included in the administration's proposed 1986 budget, to be submitted to Congress in February.

The proposal has tentative approval from President Reagan, but congressional sources said they expect it to meet with stiff opposition on both sides of the aisle when it comes up in Congress.

"It's basically a tax on the housing industry . . . and will effectively reduce the volume of loans," said Gerald R. McMurray, staff director of the housing and community development subcommittee for the House Banking Committee. "Because the mortgage lenders and savings and loans make money on the volume, they're going to be hurt when the volume of loans drops off. And if you get the mortgage bankers and homebuilders and Realtors all stirred up, you'll get a lot of Republican opposition to this proposal."

The proposal, said Ballentine, grew out of a recommendation from the Grace Commission that called for charging a user fee on debt issues from these agencies at a gradually increasing rate.

"The concept was that eventually they would be charged so much that they would break their ties with the government," said Ballentine. "This proposal is an adaptation of that, though there is no hidden agenda to keep increasing the fees. We feel this will, in no way, charge them such that they will lose the credit advantage they have as government-related agencies." Representatives of the mortgage lending industry agreed with Ballentine that the 0.05 percent user fee would not be a significant problem, but said they were worried about the policy direction in which the proposal appeared to be taking the government.

"The most disturbing thing is that these programs were set up to give middle-income and moderate-income people a benefit, but it is one they already pay for in fees," said Glen Corso, senior vice president of government agency relations for the Mortgage Bankers Association. "Now if they are going to be charged for the federal involvement, the programs will be priced out of reach of the very people they were designed to serve.

"Our concern is that this is OMB's way of getting their foot in the door. They will come back in future years and keep raising the fee until they completely wipe out this advantage."

James W. Christian, the chief economist for the U.S. League of Savings Institutions, said that his organization was concerned that the "priority on housing has clearly been lowered over the last few years," and that it would prefer a "straightforward policy" on privatization, if that is what OMB is seeking. "The five basis points are not so painful, but our position would be, please don't whittle away at us and make us worried," said Christian. "We would rather see all of it on the table."

Albert Lord, senior vice president and chief financial officer for SLMA, said the agency was unwilling to comment until it saw a "precise proposal." FHLMC and FHLBB representatives also declined to comment, and the Farm Credit Administration could not be reached. FNMA, however, was quick to attack the concept.

"We believe such a proposal amounts to a housing tax, and we are concerned about a negative effect on the cost of mortgage credit for the American home buyer and our shareholders," said a FNMA spokesman.

Ballentine said that OMB's position is that it is "difficult to argue the need for an agency that subsidizes people buying houses that cost as much as $114,000," the upper limit on mortgage loans FNMA is allowed to buy from lenders.

FNMA, however, said that its average loan was for $60,000 and that because the association paid federal taxes at the full corporate rate, it believes it has paid adequately for any advantage it has from its government ties.

"FNMA believes it should not pay a fee for carrying out its congressional mission," said the spokesman.