The government mortgage agencies got headlines recently, by cutting the interest rate on home loans guaranteed by the Federal Housing Administration and Veterans Administration. The official rate dropped to 12.5 percent, compared with a peak of 17.5 percent in October 1981.

However, most borrowers have to pay an additional one-half of 1 percent for the mortgage guarantee plus one "point," which means 1 percent of the face value of the loan. That makes the effective base rate around 13 percent, according to the Mortgage Bankers Association, compared with 14 to 15 percent on most conventional mortgages. (Under recent legislation, FHA borrowers will soon have to pay their insurance fee in a lump sum, in advance.)

But there's no free lunch in the mortgage market. A lender won't make an FHA or VA loan unless he can get the same effective interest rate that is charged on the conventional market. So what does he do? He charges three or four points on the FHA-VA loans instead of only one point. That raises your cost.

By law, a mortgage applicant cannot be charged more than one point. If the lender demands four points, the seller must pay the extra three. "But no matter what the law says, the buyer of the house winds up paying all the points," said Jack Reed, senior editor of the Real Estate Investing Letter. That's because the seller tacks the cost of the extra points onto the price of his house.

This does not happen in all cases. If the real-estate market is weak and the house has been for sale for a while, the seller may be forced to pay the extra points.

If you plan to get an FHA or VA mortgage, you should do your best to get the seller to assume at least some of the added points. The lawyer who handles your closing should do the negotiating for you. In states where real-estate brokers can handle the house closing, emphasize to the broker that you won't do the deal unless the seller pays some or all of the points.

But if you're the seller and have a desirable house, you can probably force the buyer to pay all the points.

FHA and VA mortgages have several advantages over conventional home loans:

* They cost a little less, if you can get the seller to assume some of the points.

* They generally let you buy a house with a smaller down payment than conventional lenders require. In many cases, eligible veterans can buy houses with no down payment at all.

* You can get a fixed-rate, 30-year mortgage, whose terms don't change over the life of the loan. Both FHA and VA also guarantee certain types of flexible-payment mortgages, but many home buyers prefer the certainty of fixed payments.

* An FHA or VA mortgage is automatically assumable. If you have a low-rate mortgage, the buyer of your house can assume it at no increase in monthly payments. This makes it easier to sell your house.

Nevertheless, FHA and VA mortgages do have some disadvantages. They often require a lot of paperwork, especially if guaranteed by the FHA. As a result, many lenders don't like to write them and many home sellers don't like to keep their houses off the market while waiting for your FHA mortgage to come through.

Also, there are effective limits on these loans. You can borrow no more than $90,000 on an FHA mortgage, which may not be enough for some buyers. The VA guarantees no more than $27,500 of the total loan, leaving the lender to set the appropriate maximum loan.

Both the FHA and VA insist on appraising the house before purchase. If you agreed to pay more than the appraised value, you may not be able to get as big a loan as you need.

FHA loans are available to anyone able to qualify for a conventional mortgage. But to get a VA loan, you generally have to have served for at least 90 days in the armed forces during specified wartime periods, or more than 180 days during peacetime. Peacetime soldiers also must have served the entire term they orginally signed up for.

Unmarried surviving spouses of veterans who died in service or from service-connected disabilities also can get VA loans, as can those whose spouses have been captured or are missing in action.

Even if you have used your VA loan, you can borrow again if you sold your house and repaid the loan or if you used less than the most recent loan guarantee authorized by Congress. All veterans should check with their local VA office. They may be eligible for more help than they thought.