In both of his Annual Economic Reports to Congress Kennedy said that he had ordered the Treasury to cease producing silver certificates. And in those Reports he requested that the Fed to replace the withdrawn silver certificates with Federal Reserve Notes. Halting the use of silver in coinage is a natural consequence of the decision to de-monetize silver. He considered silver to be an industrial metal.
Page 32 of the 1961 Report
and page 25 of the 1963 Report