Havering councillors rejected the plans last month due to concerns about the proposed tower blocks of up to nine stories.
In response London's deputy mayor for planning, regeneration and skills, Jules Pipe, has called in the planning application with a view to pushing it through.
Countryside Properties and London & Quadrant Housing Trust (L&Q) were chosen in January 2016 by the then-mayor Boris Johnson to take forward the regeneration of Beam Park, including a new train station on the C2C line and community facilities on the 29 hectare site that sits alongside the River Beam.
The site straddles the border of two boroughs. Barking & Dagenham Council approved the development but Havering Council said the height of the buildings would harm the character of the local area.
The potential development sits in the London Riverside Opportunity Area, which has been identified as having the capacity to accommodate at least 26,500 new homes and 16,000 new jobs.
Deputy mayor Jules Pipe said: “This is a large, very important site and the application to develop it includes nearly 3,000 homes along with a range of other uses. Having weighed up the evidence available to me and given its importance, I have decided to call in this application so it can be subjected to further scrutiny.”
The deputy mayor will consider the application at a public hearing at City Hall later in the year.