For most of its 10 years, the tiny federal agency that protects America's dolphins and whales has been the preserve of scientists.

But the Reagan administration has introduced a foreign species into the Marine Mammal Commission -- politics.

It began last year when the White House appointed James Nofziger, a California animal scientist and brother of former White House political director Lyn Nofziger, as chairman of the commission.

The choice was made without consulting the National Science Foundation, the National Academy of Sciences and the Smithsonian Institution, which by law are supposed to submit nominations for the White House to choose from.

Now, according to several administration officials, the White House is unhappy with its appointee and preparing to replace him with another politically well-connected person -- Marcia Wilson Hobbs, daughter of California real estate investor William A. Wilson. Wilson is a member of President Reagan's "Kitchen Cabinet" and currently U.S. ambassador to the Vatican.

The Hobbs appointment was to be announced yesterday, according to several administration officials. However, following an outcry from environmentalists and scientists, the announcement was canceled, and one official said the White House may appoint someone else.

Scientists say they fear that the three-member commission, long reputed to be a determined watchdog over private projects and government programs that threaten ocean mammals, will now become more devoted to administration programs.

Hobbs has no formal scientific training, according to administration officials. Her wildlife experience comes as head of the Greater Los Angeles Zoo Association, a non-profit group, according to officials, who stressed that she has gained wide respect as "a tremendous fund-raiser" and a "quick study."

Concern over the Hobbs choice also came from an unlikely quarter -- James Nofziger, who said that he considers it "desirable and essential" for commissioners to have strong scientific backgrounds. He added, however: "I don't think those people the White House are interested in what my concerns are because they don't like me."

Nofziger, who holds a PhD in animal science, said he had a run-in with the administration when officials pressured him to dismiss the commission's longtime executive director, John Twiss. Nofziger said he refused because "Mr. Twiss is a highly qualified individual who runs a tight ship, the sort of person we should have lots of in government instead of just a few."

Under Twiss, the commission has raised concerns about Interior Secretary James G. Watt's offshore oil development plans, Florida real estate development that threatened the manatee, and Hawaiian development that posed a danger to the monk seal.

Nofziger said the White House has not told him of any plans to replace him. He was appointed to fill an unexpired term as chairman, but expected at the outset to be reappointed to a full three-year term.

He emphasized that "I am committed to this administration and I just believe this appointment will create problems for them -- problems that could be avoided."

Government scientists and environmentalists questioned yesterday whether Hobbs' appointment would conform with the 1972 federal law creating the commission, which requires members to be "knowledgeable in the fields of marine ecology and resource management."

The NSF, the science academy and the Smithsonian did interview Hobbs -- at the request of the president's Council on Environmental Quality -- but only the CEQ sent her name on to the president.