Gowling is struggling and manager Andy Hessenthaler is likely to call upon Garry Richards - who replaced the central defender in midweek - should he fail to recover.
While the Gowling news is a blow, Gillingham have also received several boosts on the injury front.
Tony Sinclair is scheduled to resume full training on Monday after a foot complaint, while Andy Barcham trained for the first time on Thursday following an ankle injury.
Dennis Oli returned to action in the midweek draw with Stevenage after a two-month absence with an ankle problem and is in contention for a start after coming off the bench.
Luke Rooney and Curtis Weston, who were also substitutes at the Lamex Stadium, are pushing for starts.
Source: PA
Source: PA