On the morning of 6 January 1940 the City of Marseilles was damaged by a mine, laid on 12 December 1939 by U-13, 1.5 miles southeast of Tay Fairway Buoy, River Tay. The ship had just taken a pilot aboard when the mine exploded under her bridge, stopping the engines and causing a list of 10 to 15° to starboard. The crew began to abandon ship, but two lifeboats had been destroyed by the explosion and another capsized during launch, throwing the 14 occupants into the water. One crew member was lost. Screened by a Hudson aircraft (224 Sqdn RAF), the survivors were picked up by the pilot cutter, a RAF crash launch from Tayport and the Broughty Ferry lifeboat Mona and landed at Broughty.

The abandoned City of Marseilles was boarded by crew members of HMS Cranefly (FY 539) (Skipper H.B. Soames, RNR), HMS Sturton (FY 1595) (Skipper W. Buchan, RNR) and the harbour defence patrol craft HMS Suilven and soon thereafter her officers and a pilot returned to the vessel aboard Mona. The next day, the vessels towed her to Dundee where temporary repairs were made. The ship then continued to the Clyde for repairs and returned to service in April 1940.