The operators of two former food stamp outlets in the District were indicted by a federal grand jury here yesterday on charges of embezzling a total of $290,000 in food stamp money.

The unrelated indictments were filed against Wayne P. Miggins of 1808 C St. NE who owned the Xavier Furniture Co. and Ulysses S. Fowler, of 710 Roeder Dr., Silver Spring, who was manager of the D.C. Business Federal Credit Union. Both businesses are now closed.

Assistant U.S. Attorney Eric B. Marcy of the fraud division said the indictments were part of a continuing federal investigation into the manner in which food stamps have been dispensed in the District. The U.S. Agriculture Department program is administered here by the D.C. Human Resources Department.

Earlier in the investigation, the bishop and pastor of a small Southeast church that operated food-stamp outlets pleaded guilty to embezzling $250,000 in food-stamp money. They were given jail terms of six months each.

Yesterday's charges involved the manner in which the two outlets deposited money they had collected for food stamps. Federal regulations require that the money be deposited weekly in a Federal Reserve bank by the outlet, or more often if the outlets have collected more than $1,000. Miggins was charged with lagging by up to four months in his deposits, and commingling those funds with money belonging to the furniture business, a Georgia Avenue boutique he owns and other businesses.

Investigators said Miggins was told several weeks in advance that his business would be withdrwan as a food-stamp outlet, but that by the time it was shut down in July, 1975, he was still $203,000 in arrears in his deposits. The furniture store was located at 1401 North Capitol St.

Persons familiar with the investigation said the store was removed as a food-stamp outlet by DHR when the agency found it never had a survey bond. Such a bond should have been required before, it became an outlet, investigators said.

Fowler set up a separate account for money collected for food stamps at the D.C. Business Federal Credit Union, 4029 South Capitol St., but then failed to deposit with the federal government all the money he collected, according to the charges.

When the shortage of funds was discovered, Fowler owed the federal government $87,000, investigators said.The credit union subsequently was put into receivership and its funds liquidated. It shut down in April, 1975.

As food-stamp outlets, the two locations were among several in the city that dispensed food stamps to persons who came there with "authorization-to-purchase" cards issued monthly here by the Department of Human Resources. Recipients would turn in that card and the required cash amount, and get the amount of food stamps for which they were eligible.

More than $1 million is reportedly unaccounted for in the District alone under the food-stamp outlet programs.