A senior Commerce Department official who oversees automobile trade policy recently asked Japanese car manufacturers to consider hiring him to form a trade association to represent their interests, agency officials said yesterday.

Robert E. Watkins, deputy assistant commerce secretary for automotive affairs and consumer goods, made the proposal in a Sept. 23 letter that warned of "protectionist and xenophobic political action" that could hamper the U.S. sales and operations of Japanese car manufacturers.

Marilyn Wagner, assistant general counsel and the Commerce Department's ethics officer, said Watkins did not clear the letter with her office before sending it.

Last week, Watkins decided to recuse himself from any decisions involving automobiles and furniture after receiving a response to a job solicitation he made to the furniture industry, she said.

Watkins' letter included his resume, a proposed charter for the new trade association and concluded by saying: "If you believe this proposal has merit, I am most eager to discuss it further.

"I believe I am uniquely qualified to establish and lead an automotive association committed to market principles," Watkins' letter said

The letter outlined the political and legislative pressures that Japanese car and auto parts manufacturers face as Congress seeks ways to reduce the U.S. trade deficit with Japan.

The strategy of building of domestic manufacturing plants to make foreign cars "is succeeding only partially as protectionist efforts attempt to discredit the contribution of 'transplant' operations," the letter said.

Watkins also noted that there was pressure "to restrict the use of imported components, to impose discriminatory disclosure requirements, to limit foreign trade zone benefits and even to prohibit further foreign direct investment in U.S. production."

Wagner said Watkins did not show the letter to her office before he sent it to Japanese auto manufacturers.

She said her office would have advised Watkins not to send the letter because of his position overseeing automobile trade policy.

But Wagner said Watkins had not violated federal ethics laws by sending the letter.

"While that letter might sound bad, I don't think flooding the area with this kind of letter is a violation of law," she said. "He did come down as soon as he got a response."

Watkins did not return a reporter's telephone calls.

John Moller, a Washington lobbyist who represents Nissan's assembly plant in Tennessee, said he received a copy of Watkins' letter, as did Nissan USA.

The letter was also sent to Honda, according to a department official.

In the enclosed resume Watkins, who has held his current position since 1984, cited his recommendation to President Reagan to drop the U.S. request for Japan to continue its voluntary limit on the cars it sends to the United States.

Japan continues to limit to 2.3 million the number of cars it exports each year to this country, even though the Reagan administration did not request that it be extended last spring.