The Reagan administration's choice to head the perennially beleaguered Institute of Museum Services, a tiny, $21.5 million agency that has been called "a freckle on the federal landscape," appeared before a Senate confirmation panel yesterday to explain why she should get the job despite the fact that she has no museum experience.

Lois Burke Shepard, 47, a Potomac real estate agent, former high school teacher, Reagan-Bush campaign worker and chairwoman of a voters group known as Republicans Abroad, also was questioned by members of the Senate Labor and Human Resources Committee about her willingness to fight for an agency that the Reagan administration has been trying to eliminate since 1981.

"I was asked by the president to take this assignment because of my administrative ability and not my museum background," Shepard said, adding that she did not think museum experience was necessary because the agency is not a museum. "It is a federal agency which makes grants to museums," she said.

Shepard said that her years overseas as the wife of a Foreign Service officer gave her a special interest in preserving America's heritage: "I was proud to be able when walking through the many museums of Greece or Italy, Singapore or Bangkok to not only appreciate their treasures, but also to discuss with my hosts the vast array of treasures we have in our own country."

Shepard's nomination to the $68,700-a-year post has been criticized by Rep. Cardiss Collins (D-Ill.), chairwoman of the House subcommittee that oversees the IMS. Collins recently wrote to the White House to register "deep concern" at Shepard's qualifications:

"Would we not think it strange to appoint someone with no medical knowledge to head FDA or someone equally ignorant of aeronautics and aviation to head NASA?

"Experience as a high school teacher hardly qualifies one to assume the administrative burdens inherent in a $21.5 million agency responsible for supervising federal grants to museums and cultural institutions in all 50 states," Collins wrote.

*As chairwoman of Republicans Abroad -- the voter registration arm of the Republican National Committee for Americans overseas -- Shepard was responsible for a $200,000 budget and successfully lobbied Congress to increase the federal income tax exemption for citizens living abroad.

* The Institute for Museum Services doles out federal grants to the nation's museums and zoos for operating costs such as fuel, light and security. The Reagan administration would like to see private philanthropy do that job, and since 1981 it has tried to eliminate the agency. Last year, the Reagan budget proposal slashed the IMS budget to $292,000, just enough to close out operations, but Congress once again prevailed and set the budget at its present $21.5 million.

The Reagan budget for 1986-87 will be released next week, and because there have been rumors that the administration may once again propose draconian cuts to the agency's budget, Senate Labor and Human Resources Committee members Claiborne Pell (D-R.I.) and Paul Simon (D-Ill.) sought assurances from Shepard that she would fight to keep the agency alive.

Shepard declined to comment on the agency's future, but described as "noble" its role in helping museums conserve and display the nation's historic, scientific and cultural heritage. She said she thought it "terribly important" to solicit private money as well.

Former IMS director Susan Phillips, now in the White House's Office of Presidential Personnel, reportedly had lobbied hard to give the nomination to the agency's current acting director, Monika Edwards Harrison.

Shepard's husband William, a retired Foreign Service officer, is seeking the Republican nomination for the House seat being vacated by Maryland Rep. Michael Barnes (D).