Senate and House conferees, in defiance of a shutdown move by President Carter, agreed yesterday to provide funds to keep the new military medical school at Bethesda open for another year.

Although the action could be challenged on the House floor, it seemed likely that yesterday's decision by a joint Senate-House conference committee would prove final.

The conferees agreed to accept the Senate version of a pending supplemental appropriation bill, which contains $12.5 million for the school, over the House version, which provides no funding.

The House rarely overturns actions of its Appropriations Committee whose members served on the joint conference committee.

Yesterday's decision on the medical school - officially called the Uniformed Services University of the Health Sciences - was unusual. It provides funds to maintain activity during the 1973 fiscal year, which starts Oct. 1, 1977, in a supplemental bill that is designed to provide extra funds for various agencies and the District of Columbia for the remaining six months of the 1977 fiscal year.

Sen. J. Bennett Johnston (D-La.), who convinced the Senate that the money should be provided, said this course was taken to remove any anxiety among the faculty and both current and prospective students over the future of the institution.

Two buildings are under construction on the grounds of the Bethesda Naval Hospital, and 32 students are taking classes in temporary quarters. The school is intended to train specialists in military medicine.

President Carter recommended the shutdown of the school as an economy measure. His proposal was among recommendations sent to Congress on Feb. 22 - about a month after he took office - for changes in the budget that had been submitted previously by President Ford for the 1978 fiscal year. Ford's budget contained money for the school.

There was no immediate reaction from the White House to yesterday's action.

In other actions, directly affecting the Washington area, the conference committee agreed to spend $4.5 million to repair the leaky roof of the John F. Kennedy Center for the Performing Arts and to add $16 million to the federal payment to the D.C. government.

The city had sought $20 million. The conferees also agreed to provide the first $846,000 of D.C. subsidy for the Metrorail system, which the city government did not ask for.