The inclusion of traditional Chinese medicine in the free trade agreement between Australia and China is a step backwards for the health system and for science, one critic warns.

Chinese medicine was the subject of a side letter from Australia's Trade Minister Andrew Robb to the Chinese government, which outlined plans to strengthen cooperation on traditional medicine and could open the door for hundreds of contractual service providers from China to be officially registered to work here.

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Professor of neurophysiology and co-founder of the group Friends of Science in Medicine, Dr Marcello Costa, said the agreement would give unwarranted legitimacy to Chinese medicine.

"It's a tragedy for Australian science," Dr Costa said.

"It's almost like going back to Greek medicine or to old European medicine, there's no reason why we should take that with a smile."

But the acting CEO of the Australian Acupuncture and Chinese Medicine Association, Judy James, has welcomed the deal.

"We do know that the Chinese government has set globalisation of traditional Chinese medicine as a major priority and they've invested a lot of funding into this process," she said.

"We are delighted that the Australian Government has recognised Chinese medicine as important at the highest level of international engagement."

Ms James rejected suggestions that the deal could have a negative effect on the quality of healthcare in Australia.

"All I can say is there is a growing demand for the use of our services, we are registered health professionals, and there's a significant body of evidence to support our practice," she said.

However, exactly how the agreement will influence medical practice in Australia remains unclear.

"It may have an impact," Dr Costa said.

"Not much economically, but it will certainly change the attitude of many people going back to these medicines."

Prime Minister Tony Abbott said the "history making" free trade agreement would "change our region for the better".