Two legs dumped at a Newcastle waste site came from a health facility in New South Wales, the state's Health Minister says.

On Tuesday, a Summerhill Waste Management Centre worker found two surgically removed legs in general rubbish.

It sparked an investigation by environmental, health and council officials.

Health Minister Jillian Skinner said preliminary investigations had confirmed the legs came from a New South Wales Health facility, but she did not say which one.

"Staff at NSW Health pathology and John Hunter Hospital are assisting the EPA as it leads the investigation into how the clinical waste came to be left at the depot," she said.

She reiterated that the body parts were left at the depot in contravention of environmental and waste legislation.

"The community has the right to expect that human body parts and tissue are disposed of in an appropriate and respectful manner at all times," she said.

"On this occasion they were not and that is unacceptable.

"If a NSW Health service or a private waste disposal company contracted by NSW Health is found to have been responsible for the breach, NSW Health will act immediately to ensure such an occurrence is not repeated."

NSW Health Minister Jillian Skinner has confirmed that two severed legs found in a NSW dump came from a state health facility. ( AAP: Dan Hinbrechts )

The ABC was told the John Hunter, along with two other private hospitals in the Newcastle and Lake Macquarie area, are the only ones with specialised surgeons who perform such amputations.

A NSW Health spokeswoman said public health facilities and private contractors they engage are legally required to comply with the NSW Government directive Waste Management Guidelines for Health Care Facilities when it comes to the disposal of clinical waste, including body parts.

"Using a facility that is licensed by the EPA to dispose of human waste is the only legal practice available in NSW," she said.

"All contractors engaged by our public health care facilities to carry out the disposal of clinical waste must be licensed by the EPA. These are typically private businesses.

"Processes for the disposal of human tissue and facilities such as incinerators used to dispose of human tissue are approved and licensed by the EPA.

"NSW Health would expect body parts to be predominantly processed in the Sydney incinerator."