State general manager Nial Stock said proceedings for the proposal were before the State Administrative Tribunal for further consideration.
"The JDAP decision is disappointing as SITA remains confident the landfill is a safe, suitable and appropriate development for the proposed site," Mr Stock said.
The JDAP first considered the project in April last year but held another review of the proposal following discussions before the SAT.
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READ NOWMr Stock said a new works program submitted to the Department of Environment Regulation (DER) included significant reductions in the landfill footprint and total volume of waste.
"We also re-forecast the `life of the facility from approximately 37 to about 20 years," he said.
The Shire of York has repeatedly refused the landfill proposal, strongly opposed by the Avon Valley Ratepayers Association.
Protesters urge the community to "Stop 40 Years of Perth Rubbish in York" – their Facebook title – and to raise the environmental concerns.
They say the latest JDAP narrowly upheld the original decision in a three-two vote not to allow the landfill site because of planning issues.
"This decision (proposal) should be appealed by all members of the public for environmental reasons," say the protesters.
A Department of Environmental Regulations (DER) officer present at the meeting stated the DER had approved the revised landfill proposal.