Hughes, who tied Hiroki Kuroda for the team lead in wins last season, suffered the injury while covering first base in a fielding drill on Monday.
"There's always a little bit of concern, but it's in his upper back, not his lower back,'' said Girardi, who indicated the injury was between Hughes' shoulder blades. "You're a little more concerned about the lower back lingering, but until it's gone, it's gonna linger.''
Hughes, who left the complex before the clubhouse was opened to the media, missed three months of the 2011 season with shoulder soreness but rebounded last season to post a 16-13 record and 4.23 ERA.
This winter, he signed a one-year, $7.15 million contract -- more than double the $3.2 million he made in 2011 -- and came to camp penciled in as the No. 4 starter behind CC Sabathia, Kuroda and Andy Pettitte.