Part of the £5.5 billion Liverpool Waters development, the Plaza 1821 and Hive City Docks towers by Hodder and Partners and Brock Carmichael Architects were granted approval despite ongoing concerns.
Renderings of the pair of towers show their height far exceeding that of neighbouring buildings, breaching one of the conditions for the site to retain World Heritage status.
The World Heritage Committee is now considering the site's removal from the World Heritage List.
"We work on the basis on what we call the statement of Outstanding Universal Value (OUV), which in the case of Liverpool specifically underlined the adding of any new construction in the property should not exceed that of structures in the immediate surroundings," the head of the UNESCO's Europe and North America Unit, Isabelle Anatole-Gabrielle, told Dezeen.
"Unfortunately since before 2011 a number of developments of high buildings have been approved by Liverpool. So now the committee are faced with a situation where the outstanding universal value of the property could not be maintained," she added.
"The logical situation is the possible withdrawing of the property from the World Heritage List, which is what was proposed by the committee last year and again this year."
The initial proposals for a series of high-rise buildings in 2011 prompted the World Heritage Committee to put the city on the List of World Heritage in Danger.
Recently the city's historic docks have seen a new wave of development, including the Royal Institute of British Architects opening of a new northern outpost.
The committee now has "serious concerns" about the threat of the Liverpool Waters scheme to the site's Outstanding Universal Value.
It members recommended stripping the site of its heritage status at a meeting in July. A decision will be made in 2018.
The 31-storey Hive City Docks tower will contain 278 apartments as well as a rooftop restaurant, and will cost £55 million to construct, while the £21 million Plaza 1821 tower will host 105 apartments.
"Our vision is to create a waterfront for the world, bringing life back to the historic docklands, and this announcement brings us closer to achieving that ambition," said Neil Baumber, a director at the developer Peel Land and Property.
Six historic trading sites in the city were inscribed on the World Heritage List in 2004 for their role in the growth of the British Empire.