Spokesmen for the housing industry expressed shock and dismay yesterday that the Senate Budget Committee had restored a package of fees and fee increases on federal loan programs after having earlier voted it down.

The industry has been complaining loudly about the fees ever since the Reagan administration proposed them, and trade association officials plainly thought they had them beaten in the committee. But in the late-night negotiations Wednesday, the fee package was included in the budget proposal adopted by the committee. Under the version the panel approved, borrowers under the Veterans Administration loan guaranty program would pay 3.8 points -- up from 1 point under present law -- for a VA loan.

In addition, borrowers under the Federal Housing Administration home loan program would pay 5 points instead of the current 3.8. The Federal National Mortgage Association and the Federal Home Loan Mortgage Corp. -- as well as agencies handling revolving farm and student loans -- would pay an annual fee to the Treasury on all their debt, and the fees paid by lenders to the Government National Mortgage Association would rise.

A point is equal to 1 percent of the loan amount; thus, one point on a $50,000 loan is $500.

The fees and increases approved by the committee are less than the administration had sought, but representatives of the mortgage bankers, Realtors and Fannie Mae all characterized the plan yesterday as a disguised tax increase that is potentially very damaging to housing.

"On Wednesday the Senate Budget Committee voted, 15 to 6, to reject the so-called user fee on Fannie Mae, Freddie Mac and the others . . . . We had every reason to believe that the discussion that we had had with members of the committee to point out to them how unwise, counterproductive and how harmful . . . this tax would be had had their effect, and 24 hours later we find that this proposal is included in this deficit reduction package," said David O. Maxwell, chairman of Fannie Mae.

Maxwell said the fee on Fannie Mae's debt, which would begin at 0.05 percent and rise to 0.083 percent in fiscal 1987, would cost the congressionally chartered corporation as much as $80 million a year before taxes at the higher level. Fannie Mae posted an after-tax loss of $57.4 million in 1984 after turning a $75.5 million profit in 1983.

Maxwell, Robert Spiller, head of the Mortgage Bankers Association, and Jack Carlson, chief economist of the National Association of Realtors, met with reporters on the issue. They agreed that the fees are really a tax increase, despite President Reagan's assurances that there will be no new taxes.

"You can cut it any way you want, it is a new tax," Spiller said.

He added that he believes the fee increase on VA loans would kill that program. He said that under current market conditions, lenders already are charging 6 points to bring the loans up to market yields -- these are known as discount points -- and 2 points for origination fees. Adding the new fee, "one would be talking 11 to 12 points to a veteran," he said.

"With a 3.8 fee on the VA, that basically will wipe out the home loan guaranty program," he said.

Association officials agreed that there is still an excellent chance that Congress will drop the fees. Although the FHA increase can be done administratively, Secretary of Housing and Urban Development Samuel R. Pierce Jr. has said that HUD will not do so unless Congress passes legislation needed to boost the VA fees. Congress' Veterans Affairs committees have not shown much enthusiasm for the increase.

Likewise, HUD will not raise the Ginnie Mae fees unless Congress authorizes the Fannie Mae and Freddie Mac rises. Lobbyists noted that the needed legislation still has many hurdles to clear.