A planning meeting that looked set to approve Broadway Malyan's massive Mann Island proposals (above) for the waterfront Fourth Grace site was postponed at the last minute so the report could be considered.
The World Heritage Site report was only lodged with the council on Monday evening.
The eight-page document also casts doubt on the future of 3XN's plans for a new Museum of Liverpool building (below), which would sit in front of the Mann Island scheme.
It has previously been claimed locally that UNESCO would consider withdrawing World Heritage Site status from the city if the developments went ahead.
While the report does not go this far, it does call for the schemes to be reconsidered.
The report recommends that the Municipal Council 'should be cautious in its decisions concerning the start of works for the National Museum of Liverpool Life and the residential and commercial buildings of Mann Island.
'The mission was confronted by considerable opposition to these projects from committed groups of citizens, demonstrating that this dossier is seen by many as being very significant.
'UNESCO recommend that the City Council makes public the results of the hearings held with these groups and the arguments in support of the new design in order to allow a more informed decision making.'
However, the council denied that the report would damage development opportunities.
A response document released yesterday afternoon said: 'Members [of the council] will need to read for themselves the full text of the report to appreciate the advice given to the City Council and [central government], but a key finding is that the outstanding universal value of the site 'is considered not to be under threat'.
The mission was also 'impressed by the planning system put in place for public and professional consultations, review and approval of development proposals, following democratic principles and a high degree of transparency'.
'However, it was recognised that the system could be improved by providing better guidance and involving more partners, in particular local communities,' it adds.