Londonderry-based Brickkiln Waste has gone into administration with 50 workers losing their jobs.
The firm’s licence was revoked by the Northern Ireland Environment Agency (NIEA) on 10 July after breaching conditions.
Derry City and Strabane District Council was forced to suspend payments to Brickkiln after it failed to fulfil contractual obligations following the NIEA’s revocation.
A spokesperson for the council said it had been working with the NIEA and other councils to resolve the processing of waste.
“Where invoices have been received by the council demonstrating that the company has met the agreed terms, these invoices have been paid in full.”
The Department of Environment confirmed that the notice suspended the acceptance of all waste to the site.
“The facility, having failed to take the necessary steps to comply with two previous notices served on the site, remained in breach of its licence conditions,” said a spokesperson.
“This further notice does not prevent the export of waste from the site and should enable the facility to put remedial action in place.”
A similar notice was served on the facility in December 2013 although this was lifted a month later following remedial work.
On 7 July, the BBC reported a fire at the Brickklin site which involved almost 50 firefighters.
In March 2014, a Shanks-led consortium, which included Brickkiln, was told that a £560m residual waste project was being stopped at the procurement process over fears of extra costs.
The project would have handled up to 140,000 tonnes of residual waste a year via an MBT facility at Brickkiln’s site in Maydown and have produced solid recovered fuel for a gasification facility.