The Mayor of London, recently back from a business-boosting China trip, has stepped in after Hong Kong-based Hutchison Whampoa became frustrated at "unrealistic demands" from the council over their Convoys Wharf project and urged him to intervene.
Their plans for the site, which has been vacant for 13 years, involve 3,500 new homes and have proved controversial, with concerns raised about buildings' height and lack of consideration for Deptford's naval heritage.
But Mr Johnson, whose Design Advisory Group advisors include the scheme's architect Terry Farrell, said: "We need to build thousands of new homes in the capital and proposals to do that at Convoys Wharf have been on the blocks for over a decade.
"Those plans deserve full and thorough consideration, and my team will work closely with the borough and the applicant to do so without further delay."
The application for the site, which has been vacant for 13 years as plans have repeatedly stalled, is set to be considered next February.
But the move has sparked outcry, with Lewisham Deptford MP Dame Joan Ruddock writing to the mayor, asking for a meeting about the site, recently placed on a global watch list of threatened heritage sites.
She wrote: "You will know that Convoys Wharf occupies the site of Henry VIII's naval shipyard and also encompasses the land on which John Evelyn had his manor house and extensive gardens.
"As such this site ought to be an archaeological and heritage jewel in London’s crown. However it was systematically overlooked until local campaigners demanded more attention was given to it."
London Assembly Member for Greenwich and Lewisham Len Duvall said: "While the mayor could have worked with the borough to progress development, as they have done for years, he cannot ignore the real concerns Lewisham was working through in the run up to a decision.
"I hope they continue to work on resolving the very real concerns Lewisham have and get a good deal for our residents."
A spokesman for Lewisham Council said: "This development is of great interest and importance to Lewisham and we are hugely disappointed by the Mayor’s decision for the GLA to act as planning authority.
"The GLA recognises Lewisham Council’s good performance in delivering new housing over recent years. We note also that the report recommends a continued close working relationship with Lewisham Council to ensure that local issues are fully considered and acknowledges that we need to secure from the developers significant local benefits should the application be approved.
"We will continue to represent local concerns and support the appropriate regeneration of our Thames waterfront to provide much needed jobs and homes."