He suffered the problem during the three-game inter-league series at Houston two weeks ago.
On its Web site Friday when the move was made before the Subway doubleheader against the New York Mets, the team said inflammation and fluid in the knee were discovered during a doctor's examination.
The knee was drained recently, but running is bothering him more than hitting.
"If I needed to play right now, I could play as long as I don't run so hard," he said. "It would help to get some rest right now and just get ready."
To date, Matsui is hitting .323 in 69 games (251 at-bats) this season with seven home runs and 34 RBI.
He has not played since June 22 in a contest at Cincinnati.
"Surgery is always the next step, but we're hoping to avoid that," Manager Joe Girardi said before Saturday's contest against the New York Mets.
General Manager Brian Cashman estimated Matsui is running "at about 75 percent now, and hopefully we can get him back to 100 percent."