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Thomas Lipscombe mentioned in his original NY Sun article about this that the Secretary of the Navy that would have given that discharge is John Warner - now a Republican Senator from Virginia.

Sen. Warner's official Senate website verifies that he was appointed Under-Secretary of the Navy in 1969 and was promoted to Secretary of the Navy and left the service and that position in 1974.

So, if we're talking about the Secretary of the Navy that would have been involved in this less than honorable discharge, it will have to be Senator Warner. However, when Lipscombe asked him to comment he said he had no recollection about Kerry. Maybe he's come around.