Watson said, quote: "From my standpoint, we don't need that type of distraction."
Watson, who's a former GM of the Astros and New York Yankees, said he didn't anticipate being overruled by higher-ups.
Clemens has been accused by his former trainer, Brian McNamee, of using performance-enhancing drugs.
Clemens repeatedly denied the accusations and filed a defamation suit against McNamee.
Clemens apologized Monday for unspecified mistakes in his personal life.
Clemens played for the U.S. team in the inaugural World Baseball Classic in 2006.
He went 6-6 with a 4.18 ERA for the Yankees last season.