The Panama Canal, linking the Atlantic and Pacific Oceans, is doing an almost embarrassingly high business in the midst of Panama's crisis, an official of a bilateral commission that runs the waterway says.

Richard A. Wainio, chief of economic research and market development for the Panama Canal Commission, called it a strange operation that is running smoothly despite tough political problems between Panama and the United States

because neither country wants to jeopardize operation of the canal.The commission, made up of five American and five Panamanian government representatives, was set up under terms of a 1977 treaty that eventually will turn the canal over to Panama in 1999.

There is an impasse over canal revenues because the United States refuses to recognize the military rule of strongman Gen. Manuel Antonio Noriega and is trying to force him out as chief of Panama's defense forces.

It has been withholding payments of approximately $18 million in canal

revenues to the Noriega government, ever since the general ousted President Eric Arturo Delvalle on Feb. 26. Gen. Noriega is under indictment in U.S. federal courts on drug trafficking charges.

Mr. Wainio said that canal expenses during the rest of 1988 are expected to wipe out any revenue surplus.

The treaty specifies that any surplus revenue, up to $10 million annually during the life of the treaty, be turned over to the Panamanian government.

The United States paid Panama nearly $79 million for use of the canal in fiscal 1987. Payments in fiscal 1988 are expected to total $80 million.

For now, the Reagan administration is depositing the payments in an escrow account in the United States.