The EPA said on Wednesday it had issued a $31,500 penalty to three subsidiaries of the waste company after coordinated visits at Rutherford, Wetherill Park and Windsor in June.

The company was fined $15,000 over the condition of the site at Kyle Street, Rutherford.

EPA regulatory operations director Steve Beaman said inspectors found several storage tanks stockpiled on "unsealed, uncovered and poorly contained areas" at the Hunter premises.

Mr Beaman said an oil tank containment area had three leaks and there were several holes in the roof, which also had "considerable rust".

"Some of the drums were stacked in a way which created a risk of them falling and spilling," he said.

"Together with poorly maintained containment areas, this created the potential for environmental harm.

"Some containment areas used to store drums had holes which meant that if the drums leaked, the spill would not be contained and could leak to soil or nearby waterways."

The penalty comes after the environmental watchdog took action against Cleanaway over the Rutherford site in 2016 due to incorrect storage of waste.

The company was fined $15,000 earlier this year for storing 15,000 tonnes of waste from a container deposit scheme at Beresfield without a licence.

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