Victoria's environmental watchdog has charged the operators of a soft plastics recycling company, alleging the company secretly stockpiled plastic bags.

The REDcycle scheme was paused in November, after the company announced it could no longer recycle the plastics it was collecting at major supermarkets across Australia.

The EPA found 3,000 tonnes of soft plastics in nine warehouses across Melbourne's north, west and south, and in north-east Victoria.

The plastics are in two warehouses in Tottenham, as well as warehouses in West Footscray, Truganina, Williamstown North, Campbellfield, Tullamarine, Dandenong South and West Wodonga.

The Environment Protection Authority (EPA) charged RG Programs and Services Pty Ltd, the operators of the REDcycle program, with three counts of failing to comply with an Information Gathering Notice.

EPA chief executive Lee Miezis said officers discovered a store of plastics in a warehouse in Williamstown North in May, and required the company to disclose the location of other plastics stored across the state.

"What we allege is they did not disclose all the information," he said.

"They did disclose some addition sites, but other sites have been identified directly by the EPA investigators, talking to logistics companies and trucking companies and other parties."

The maximum penalty for each charge is more than $165,000.

"It is an offence under the act, that when the EPA is investigating matters people are honest and they provide all the information," Lee Miezis said.

"It helps us protect the community and it helps us protect the environment."

He said the EPA had issued five notices to warehouses to make sure the plastics were stored safely, so there was no fire risk.

The EPA is working with the warehouses and the Department of Land, Water and the Environment to find a way of recycling the plastics.

The ABC has contacted REDcycle for comment.