The stadium plans are linked to a separate planning application for the redevelopment of the club's existing Goodison Park stadium. The club has said the redevelopment plans for Goodison Park could include new homes plus health, leisure and education facilities and community meeting rooms.
Now, however, Historic England has asked for the stadium plans to be called in by the housing secretary.
A statement issued by the body said it considered that the proposal to infill the dock "would fundamentally change its historic character as a water-filled basin which so clearly tells the story of the docks and has contributed to its status as a WHS".
"The loss of the water would result in substantial harm to the significance of the Grade II listed Bramley-Moore Dock and cause harm to the WHS", the statement said.
It added that, "due to the impact of the proposals on a WHS, which has the highest level of heritage protection and is internationally significant, we regrettably think that this application should be determined by the secretary of state and will ask for it to be called in for his determination".
The statement also said it has advised "that the application should be refused, unless the decision-maker concludes that the public benefits would outweigh the damage to Bramley-Moore dock and the harm to the WHS which the proposals would cause".
A heritage statement submitted by the football club as part of the planning application said it "considered that whilst the proposals would have a harmful impact on heritage assets within the site and on the Stanley Dock Conservation Area, the impact on the overall authenticity and integrity of the whole WHS would be less than substantial".
It also said there is "a long tradition of the infilling and reuse of Docks within Liverpool Docks throughout the WHS, with the Three Graces built on former Docks as well as The Museum of Liverpool and the Liverpool One development".
A statement issued by the club said that "local politicians, the more than 60,000 people who took part in our public consultations, our business community and third sector stakeholders all have a different view [to Historic England] and fully support our proposals".
"The local public has told us – in huge numbers – that they believe the public benefits of our plans far outweigh the suggested level of harm to the heritage assets", it said.
The club statement said the council could determine the application "towards the end of the year".
"The detail of this determination is likely to dictate whether the application will also need to be reviewed by central government", it added.
The Ministry of Housing, Communities and Local Government was asked if it had received the call in request and if any decision had been taken but had yet to respond by time of publication.
Have you advised on, or secured, a recent major permission? We want to know about big housing, retail and leisure, and commercial and industrial schemes approved between 1 June - 31 August 2020 for our next Biggest Permissions report. To qualify, schemes should be above the following thresholds: 500 homes; 5,000 square metres of retail or leisure space; or 20,000 square metres of commercial or industrial space. To get involved, or for more details, please email eleanor.kahn@haymarket.