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A local government authority is suing the head of the Department of Environment and Conservation in a bid to recoup more than $1.7 million in waste fees it claims should never have been charged, plus interest.

The Eastern Metropolitan Regional Council launched the action against DEC chief executive Kieran McNamara, claiming it was wrongly slugged almost $1.7 million through the waste levy.

The Supreme Court writ claims the DEC incorrectly classified more than 65,000 tonnes of waste disposed in landfill at Red Hill between April 2009 and September 2012 as subject to the levy.

It was lodged late last week but has not yet been served.

"The amount . . . paid by the plaintiff to the defendant exceeded the amount of the levy due and payable by the plaintiff by $1,690,298 plus interest of $29,674 totalling $1,719,972," the writ alleges.

EMRC's acting chief executive Hua Jer Liew said the council was unable to provide any further details because the matter was now before the court.

The EMRC is a regional local government authority working on behalf of the Town of Bassendean, City of Bayswater, City of Belmont, Shire of Kalamunda, Mundaring Shire and the City of Swan.

It provides services in waste and environmental management and regional development.

A DEC spokeswoman said she was unable to comment because the case was before the court.

The EMRC's action comes after a Supreme Court case last year when Perth waste management company Eclipse Resources unsuccessfully argued most of its operations involved effectively recycling "clean fill" and should be exempt from the levy.

Supreme Court Justice Michael Corboy dismissed the case and upheld the department's right to apply the levy.