The Yankees manager said the right-hander, who is 0-1 with a 13.94 ERA after three starts this season, needs time to rebuild his arm strength.
"We just feel like he's going through a dead arm period," Girardi told the New York Daily News. "We don't feel that he's hurt. There are no tests planned for him, but we saw him get to 91-92 (mph) yesterday and it was like he just ran out of gas after two innings."
Hughes has allowed 16 earned runs on 19 hits over 10 1/3 innings this season.
"Something had to be done," Hughes told the newspaper. "My velocity's just not there. My arm feels dead ... This will let me build arm strength and get this right."
Girardi said veteran righty Bartolo Colon will take Hughes' spot in New York's rotation. Pitcher Lance Pendleton was called up from AAA Scranton to fill the roster spot.