The D.C. City Council, brushing aside a prediction of intense congressional opposition, decided yesterday to move ahead with legislation to eliminate city real estate tax exemptions for 38 national and local organizations.

The measure, introduced by David A. Clarke (D-Ward 1), would repeal exemptions on Washington properties granted over the years by Congress to such organizations as the American Legion, the Veterans of Foreign Wars, the Daughters of the American Revolution, the National Geographic Society and the National Education Association, with millions of members across the nation.

The full council membership, meeting as a committee yesterday, agreed to put the bill on its agenda for a preliminary vote, probably next Tuesday.

If enacted by the council and permitted by Congress to go into effect, the measure would increase the city's tax revenues by up to $1.5 million next year and $3 million each year thereafter. The smaller sum would be collected initially bacause the bill would apply only to the second of the two tax installments to be collected in the 1981 fiscal year.

The city's Home Rule Charter permits the council to amend or repeal congressionally passed legislation dealing with most local matters. However, Congress has the power to veto any council action. It has done so only once -- last December, when it overturned a council bill restricting the right of foreign governments to locate their embassy offices, called chanceries, in residential neighborhoods.

John A. Wilson (D-Ward 2), chairman of the council's finance and revenue committee, said he has been warned by Capitol Hill sources that there is a good chance Congress would veto the tax exemption measure. The resulting political problem may outweigh the additional revenue, Wilson said at a council bill-screening session yesterday.

The bill was apprioved July 3 by Wilson's committee because the revenues are included in the finalcing of the city's proposed and precariously valanced $1.5 billion budget for fiscal 1981 now pending before Congress. Wilson said he has not decided whether to support the bill when it comes up for council vote.

Any organization that would lose its tax exemption under the pending legislation would be permitted to apply for a new exemption under a general city law that forgives taxes on churches, nonprofit private schools and charitable organizations that provided services to District citizens.

Under the general law, the D.C. Finance and Revenue Department has reported that only three of the 38 affected organizations would clearly qualify for exempt status. Those are the Corcoran Gallery of Art, Howard University and Oak Hill Cemetery. Potential exemptions on six other organizations are regarded as "questionable."