There's still no word yet on how much fuel spilled as it was being loaded onto HMCS St. John's Wednesday morning.
Environment Canada has crews monitoring the clean-up. The department said it collected samples and ordered a Transport Canada fly-over of the harbour.
The powerful smell of fuel on the water was still evident several hours after the spill was reported.
The ship is anchored near Dartmouth Cove, directly across from downtown Halifax.
This is the second navy ship spill in the harbour in the past two years. There was another accident when the supply ship HMCS Preserver was being refueled in March 2011.