In 1956, Watanabe founded the Japan Philharmonic Orchestra and continued as its resident conductor until 1968.

In 1978, he once again became resident conductor of the newly reformed Japan Philharmonic Orchestra, with whom he stayed until 1983.

Watanabe was a regular guest conductor with orchestras in the United States and Europe (Kennedy 2006).

Watanabe made the first complete set of recordings of Sibelius' symphonies in stereophonic sound with the Japan Philharmonic from 1960 to 1962 for the Nippon Columbia Company (these were released on Columbia's Epic label in the United States).

He re-recorded the Sibelius symphony cycle in digital sound with the same orchestra in 1981 for Denon.