Transport Canada says inspectors are confident the MV Marathassa's deficiencies have been fixed and it meets regulations and is environmentally safe for travel.
The grain-carrying ship on its maiden voyage leaked at least 2,700 litres of fuel into the city's harbour on April 8, quickly spreading to popular beaches nearby.
Transport Canada says a thorough investigation of the fuel discharge continues and the ship's operators could face fines or prosecution if they are found to have violated Canada's shipping laws.
The federal agency says pollution recovery efforts are slowly winding down and the wildlife rehabilitation team is being demobilized.
Canada's laws ensure that polluters are held financially liable, and the operators of the MV Marathassa have agreed to pay for clean up and to appear in future legal proceedings that could lead to fines.
Transport Canada will conduct regular flyovers of the MV Marathassa as it departs Canadian waters.