Stephen Byers has stepped into the controversy surrounding the proposed 66-storey skyscraper at London Bridge, dubbed the "shard of glass".
The Secretary of State for Transport, Local Government and the Regions has written to Southwark Council instructing it not to grant planning permission without his "specific authorisation".
The letter from Mr Byers, known an Article 14 direction in planning jargon, states: "This direction is issued to enable the department to have a further period in which to consider the proposal."
Media reports suggest that Mr Byers will decide that a public inquiry should take place to decide on plans for what would be the tallest building in Europe.
On 8 March Southwark's planning committee approved the application in principle, although the borough's unitary development plan states that the Southwark "is not considered to be an appropriate area for high buildings".
Mr Byers' decision comes as London Mayor Ken Livingstone backed the Tower:
"The scheme offers significant regeneration benefits for the immediate area. At my request Southwark Council has given an undertaking to use planning powers to ensure that the high-quality architecture and design of the building can't be diluted in any way. I hope that the Government will soon also give the go ahead to the development which both the local authority and I believe will be a great addition to London."
The Mayor has previously stated that where he and the local authority concerned agree to allow a particular development to go ahead, the government should not intervene.