The Federal Emergency Management Agency's national flood insurance program has returned to the old-fashioned policy of paying claims with checks after another method created financial embarrassment recently for some St. Petersburg, Fla., residents.

What happened was that about two-dozen families, whose homes were flooded by torrential rains in June, deposited in their bank accounts something that looked like a check and walked like a check but bounced when it was handled like a check. It is called a sight draft.

Judy and David Miles received a sight draft for $5,325 and deposited it in their bank account. "It looked like a check to me," Mrs. Miles said. "I thought it was as good as a bond. We started writing checks left and right. I already ordered carpet, thinking I had the money in the bank."

When that turned out not to be the case, the Mileses had to cover the checks with their own money, a process that involved dipping into the family savings and wiping out a vacation, she said.

Jeffrey S. Bragg, head of the Federal Insurance Administration, said that "The difference betweeen a check and a sight draft is that a check is negotiable but a sight draft is only collectible. You have to get concurrence of the person who wrote it before you would issue the funds."

Bragg said he doesn't know why the agency was using sight drafts, a practice he said was initiated late in the Carter administration. "When we got here we noticed people were having troubles, and we started monitoring the situation. When we found out there were problems, we went back to checks."

Flood insurance is not generally available from the private market. The federal government provides it to homeowners after their local governments have adopted programs to preclude or restrict future construction in areas that are likely to flood.

There are about 1.9 million policyholders in 17,000 communities nationwide. The average annual premium is about $200, Bragg said, and that buys $56,000 in coverage. In fiscal 1981, the program paid $225 million in claims, but that was considered a low-claim year. In fiscal 1980, claims totaled $400 million.

Bragg's goal, he said, is to make the program self-supporting, but rate increases for premiums have been "controversial."