It follows approval by Liverpool City Council of a Â£5.5bn plan for redevelopment of the waterfront in March.
Unesco decided the scheme, involving skyscrapers, could "irreversibly damage" historic docklands.
Liverpool City Council described Unesco's move as "premature".
The plans have yet to go to the secretary of state for final approval, and could be subject to a public inquiry.
Unesco inspectors visiting the site in November 2011 expressed concerns about the height of buildings planned for the development, which would include the tallest UK building outside London.
The organisation's World Heritage Committee ruled earlier, at its 36th annual meeting in St Petersburg, that the site should be put on the "in danger" list.
The committee warned that if the project goes ahead Liverpool may entirely lose the "outstanding universal value" for which it was given World Heritage status.
They said it would significantly alter the skyline and fragment the dock areas.
A Liverpool City Council spokesman said they believed safeguards could be put in place to protect the site's heritage.
He added: "We believe that this decision is premature as the government has not yet determined whether the Liverpool Waters application can go ahead.
"The city council is continuing to discuss the plans with the developers and other interested parties and have always firmly believed that Liverpool can retain its World Heritage status while sensitively developing the derelict docklands.
"It is important to note that although this decision has been made it does not mean that Liverpool is in imminent danger of having its status removed.
"This is a long term development which will take several decades to complete and as it progresses we will continue to work to ensure that we can reach a situation which satisfies all parties."
The Liverpool Waters development would include a cruise liner terminal and thousands of apartments.
Bidder Peel Developments said the scheme could create up to 20,000 jobs.
Liverpool was awarded World Heritage status in 2004, ranking the city alongside the Taj Mahal and Stonehenge.
Liverpool's historic docklands have been added to Unesco's "in danger" list for possible removal of its World Heritage Status.