A week has passed since Waste4Fuel staff were last at the St Paul's Cray site, and it is now considered abandoned.
The Environment Agency says a fence will now be installed around it, securing the site and reducing the potential impact for trespass, arson or other anti-social behaviour.
It will also allow access for the Environment Agency and the London fire and emergency planning authority.
The fencing was one of the conditions of the enforcement notice issued to the site on July 8, but was not complied with.
It is the responsibility of the site operator, and then the landowner, to clear up the site, however the Environment Agency will be working with Waste4Fuel, Bromley Council and other partners to consider how to reduce the amount of waste left on the site to a safe level.
Chris Hazelton, environment manager at the Environment Agency, said: "We understand the frustration of local residents and we’re committed to finding a solution that will bring to an end the upset and nuisance for the community."