The ship is now heading towards deeper waters on its own power.
In the first phase, the bearing of the ship was corrected and the second phase involved the ship being towed to deeper waters, said seafaring captain Asim Iqbal.
Iqbal added that a special rope, with a pulling capacity of up to 0.1 million tonnes was used in the effort and the ship was eventually towed 2.5 kilometres out to the open sea.
An adviser of the ministry, Mahmood Molvi, confirmed to the media that the ship is now deep waters and added that the Heng Tong will now dock at the Karachi port and will be allowed to leave after its cleared by technical teams.
The adviser added that all expenses of the refloating operation will be borne by the owner of the ship.
Last month, the eligibility of SeaMax, the company operating the operation, was called into question.
According to shipping industry sources, the ship's owner hired Seamax in Pakistan through Dubai-based C-Crest to save money and Seamax hired a local company that specialises in ship breaking.
The Port and Shipping director-general objected to the operation plan and hinted at an investigation into the companies' eligibility and approval of the plan.
The owner of the ship stranded off the coast of Karachi, hired SeaMax through a company called Seacrest. Foreign salvage companies had demanded huge sums for the service.
Heng Tong's shipping agent in Pakistan was also reportedly excluded from the deal, and the ship's owner dealt with the salvage company directly.
The final push to tug the stranded container carrier Heng Tong failed on Tuesday as tides pushed the vessel back to the place from where it was dragged into the water on Monday.
The ship from Hong Kong, sailing under a Panama flag, got stuck on the Sea View Beach as it lost an anchor while approaching the Karachi Port on its way from Shanghai to Istanbul last month. Ship Agent Captain Asim Iqbal told the media that the salvage crew had managed to drag it 800 metres into the sea and were hoping to start the engine and turn on the propellers.
However, the ropes of the tug boat snapped as the mariners tied to pull the 36,000 deadweight tonnage vessel into the deep, he said. The tug boat's engine also blew up in an effort to 'tug more than it could pull'.Captain Iqbal said they have two more days to refloat the stranded vessel, otherwise, the high tides will subside with the waning moon.
Meanwhile, Heng Tong 77 Captain Umar said that the otherwise successful operation failed due to the incapacity of the tug boats. He declared that the salvage company, Sea-Max, was responsible for the failure of the operation. The tugs provided by Sea-Max were not powerful enough to do the job, he said.