The fast ferry had just left the French harbour on Monday afternoon for a crossing to Jersey when the fault was detected.
It was already operating on reduced power after developing a separate engine problem.
In a statement on its website, Condor said: ‘Condor Rapide suffered a fault with her starboard inner engine upon departure from St Malo this afternoon.
‘In order for our onboard engineering team to access the issue, Condor Rapide has returned to St Malo.’
Condor’s conventional passenger-freight ferry, Commodore Clipper, was also delayed on Monday after developing engine problems while arriving in Portsmouth.
