Communities secretary Eric Pickles has ordered a public inquiry into plans to redevelop the Shell Centre on the South Bank.
The scheme is backed by Canary Wharf Group and Qatari Diar and includes new office space for Shell.
"Having carefully considered this case, ministers have decided to call in this planning application," said a spokesman for the Department for Communities and Local Government.
"Ministers are very selective about calling in planning applications and only take this step if planning issues of more than local importance are involved.
"The process will include reviewing all relevant considerations, including the design and any potential impact on the UNESCO World Heritage site by Parliament Square."
A spokesperson for the joint venture developers, Canary Wharf Group and Qatari Diar, said: "We are extremely disappointed at this decision which will inevitably delay the project and could jeopardise thousands of jobs as well as the regeneration of the local area. It sends a very unhelpful message to developers who want to invest in London.
"The project would deliver significant local benefits including new jobs and employment programmes, hundreds of new homes including much-needed affordable and social housing, new open spaces including a park and would act as a catalyst for the regeneration of the whole of Waterloo.
"This scheme involved an extensive year-long public consultation with representatives of the local community and has been supported and approved by the London Borough of Lambeth and the Mayor of London. This is a project designed to be sympathetic to the heritage and character of this important part of London with minimal impact on historic and protected views.
"We will now make every effort to expedite the inquiry process to ensure that this important project can proceed."
Mr Pickles' decision has drawn an angry response from Lambeth Council.
"Shell is one of Britain's largest and most important employers and will act as a catalyst for further jobs and economic activity in Waterloo.
"Calling in the decision is not only bitterly disappointing but means further delays to economic growth and sends the wrong message to developers who are prepared to invest in and work with local communities."
The secretary of state's decision to "call in" the application comes as Lambeth Council, the City of Westminster and English Heritage remain in dispute about the adjacent Elizabeth House scheme which it is claimed will detract from views of the Palace of Westminster.