The blaze at the Campbellfield site in April 2019 took four days to extinguish and sent plumes of smoke into the air, causing the evacuation of nearby businesses and closing some schools.

Former factory owner, Bradbury Industrial Services, had its licence suspended by Victoria's Environment Protection Authority that March for stockpiling chemical waste, and went into administration soon after the fire.

The state's environment watchdog confirmed on Monday its clean-up of the site had been completed, with almost 6000 tonnes of waste removed during the six-month operation.

The clean-up included demolishing the site's remaining buildings and infrastructure, drainage works, removing contaminated soil and concrete slabs, and recycling 2000 tonnes of the concrete.

It is estimated to have cost about $6.5 million.

Chief executive Lee Miezis said it was a highly complex operation for staff and its contractors.

"Despite the complexities, I'm pleased to say we were able to complete the operation and are now assessing legal options to recoup what costs we can on behalf of the Victorian public," he said.

The EPA laid charges against the company in March last year over various breaches of the Environment Protection Act.

According to the EPA's website, updated last week, the charges remain before the court.

Australian Associated Press