Underscoring the increased importance of U.S. trade relations with Japan, the Commerce Department yesterday named Clyde V. Prestowitz Jr. to a newly created post as counselor to Commerce Secretary Malcolm Baldrige on Japanese affairs.

Prestowitz, who has been deputy assistant secretary of Commerce for international economic policy, will act in his new job as the principal policy adviser on U.S.-Japanese commercial relations to Baldrige and Lionel H. Olmer, undersecretary for international trade.

Prestowitz, 41, who is fluent in Japanese, has been a principal adviser to Baldrige and Olmer on trade issues with Japan and will represent them in negotiations with the Japanese. He will remain as cochairman of a U.S.-Japanese working group on high technology and continue his involment in talks with Japan over the issue of industrial targeting.

The position is an unusual one for the Commerce Department, and, according to sources, it was designed to give Prestowitz added clout in negotiations with the Japanese.

"Our trade relations are crucial to both the U.S. and Japanese economies, and I wish to stress that importance by making this appointment," said Baldrige.

Before joining Commerce in September 1981, Prestowitz had been an international trade consultant with offices in Tokyo and Brussels; worked for several corporations; served as a foreign service officer, and was a newspaper editor. He speaks five languages and has a masters degree granted jointly by the University of Hawaii and Keio University in Tokyo.