Kaplan said the decision to remove the jersey was not made to generate publicity, but was done in response to allegations of steroid use by Clemens that resulted in Wednesday's Congressional hearing where the seven-time Cy Young Award winner testified.
"It was the fact that there are a lot of unresolved issues involving Roger and it was difficult for us to give answers to the kids coming through the museum," Kaplan said.
The Yogi Berra Museum and Learning Center, which opened in 1998, offers several educational programs for youths including one that focuses on sports medicine and nutrition and examines the use of performance-enhancing drugs.
Clemens' jersey had been displayed alongside former teammates Derek Jeter and Mariano Rivera. Clemens was a member of the 1999 and 2000 Yankees championship teams.
Jeter's and Rivera's jerseys will stay in the display, Kaplan said. Both have been with the Yankees since 1995.
"In light of what's been happening, we just thought the display would be well-served by having the guys who were there from the beginning of the run," Kaplan said.
Kaplan said he decided to remove the jersey with chief operating officer Art Berke. They notified Berra of their decision and the former Yankee great "was OK with it," according to Kaplan.
Clemens and Berra are friends, and the former pitcher has played in a celebrity golf event that raises money for the museum, Kaplan said.
Clemens' spokesman Joe Householder didn't immediately return a message seeking comment Saturday.
The jersey's removal was originally reported in The New York Times in Saturday's editions.
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