The cost estimate for the Smithsonian Institution's two new underground museums on the Mall has risen in the past nine months from $50 million to $75 million, despite cutbacks in their projected size and facilities, Smithsonian officials report.

The museums for African art and Eastern art, approved in January by federal planning agencies, have been authorized by Congress but not yet funded.

Although the Smithsonian has proposed raising half the money for the new subterranean museum complex through gifts from foreign nations and corporations, Tom L. Peyton, director of facility services, said last week: "I'm sure the cost increase will bother some people on the Hill and we'll get questions about it."

The escalating cost estimate comes at a particularly bad time, Peyton said, because Congress is facing another round of budget cutbacks under the Reagan administration's austerity program.

The original $50 million estimate apparently was low "because we didn't have detailed engineering cost estimates," Peyton said, and because inflation would significantly boost construction costs by the time the planned museums would be completed in 1985.

To offset some of the building costs, the Smithsonian now plans to eliminate all underground parking and has reduced the size of the two museums by about one fifth, from 460,000 to 350,000 square feet.

Most of the African and Eastern art museums would be underground, with only two pavilions and perhaps a kiosk entrance visible in the four-acre quadrangle, or square, behind the old Smithsonian Castle where a Victorian-style garden and employe parking lot are now located.

When the Commission of Fine Arts reviewed the design changes last week, it praised the elimination of the parking lot, the courtyards and the deep "light wells" originally proposed by the Smithsonian. They are to be replaced with a less formal garden, skylights hidden in the shrubbery, and two glass-bottomed pools to enliven the park and light up underground museum hallways.

But the commission criticized the latest designs for the pavilions themselves. Drawings of the two 60-by-90-foot buildings shown to the commission depict the African museum as a domed, pink granite building with a Moroccan air, and the Eastern Museum as a green granite pavilion with a series of small pyramid roofs.

Commission Chairman J. Carter Brown termed the designs "a World's Fair solution" that detracts from the three buildings that would surround them: the Freer Gallery and the Mall's two most historic Victorian-style brick structures, the original 1855 Smithsonian Castle and the 1881 Arts and Industries Building.

Brown urged a more "Victorian eclectic" or modern design that does not attempt to be Oriental or African to mimic the art inside.

The Smithsonian will present the same designs next month to the Joint House-Senate Committee on Landmarks and in November to the National Capital Planning Commission. Peyton said there will be no changes in the designs until the other federal agencies have commented.

The Smithsonian is asking Congress for $1 million in planning funds for the two museums in fiscal 1982, and the institution hopes the administration will request $36.5 million more the following year.

Japan and Korea already have pledged $1 million each for the Eastern museum and corporate and private pledges total another $3 million. The Smithsonian plans to contribute just under $10 million from its own trust funds and is about to launch an international fund-raising campaign to raise the remaining $23 million for the museums from foreign countries and corporations as well as American donors.