Passengers from the ferry and others waiting at the port were taken to a nearby Asda car park by police as the search was carried out.
CalMac said the vehicles on MV Caledonian Isles were left on board.
Remaining scheduled sailings from Ardrossan were cancelled on Friday evening.
CalMac CEO Duncan Mackison said: “CalMac staff and crew are following emergency procedures alongside the emergency services and no injuries have been reported.
“Customers will be kept informed of the situation as it develops.”
CalMac is the UK’s largest ferry operator, running 29 routes across 200 miles of Scotland’s west coast.