WA's Health Department has revealed it has encountered "significant issues" in developing a stand-alone clinic for women seeking abortions at the new Midland Health Campus.

The State Government was forced to plan for the separate clinic after awarding a $5 billion contract to build and run the hospital to St John of God Health Care.

The Catholic healthcare provider refuses to offer pregnancy terminations or contraception services.

North Metropolitan Health Service chief executive Shane Kelly has told a budget estimates hearing the Government did not factor in the extra cost of the additional clinic.

"We don't have that information, it is not planned that the state would plan and build a facility on the Midland Health Campus," he said.

But Health Minister Kim Hames has denied taxpayers would foot the bill for the abortion clinic.

When asked on 720 ABC Perth whether the Government would be left significantly out of pocket, Dr Hames said he expected a private provider would shoulder all infrastructure costs.

"Our proposal is that we'll provide the land, and the private sector build it," he said.

"As part of our expressions of interest, that's what we're seeking, and we would fund those services that we wish to be supplied that would previously be done in the public hospital."

Mr Kelly also told the hearing the services agreement between the Government and St John of God Health Care had made developing the site difficult.

In the agreement, the health care provider stipulates the clinic must have a separate entrance and car park, "which is away from any hospital entrance or car park".

It also requires the clinic be separately fenced "with no direct access from the hospital or car park" and "not be connected to the hospital by any shared utility or infrastructure".

Mr Kelly said those limitations had hindered the process.

"They're unable to share services and infrastructure with a provider of services that is contrary to Catholic healthcare provision," he said.

"So, there are access issues which make for the development of infrastructure on that site problematic."

The clinic will also offer vasectomies and contraceptive services.

The contract with St John of God is for 23 years and the 307-bed hospital is due to open in November 2015.

A St John of God spokeswoman said the group would meet the terms of its contract.

"St John of God Health Care signed a contract with the State Government of Western Australia in June 2012 to provide all the services required by the Government when they set out the tender for Midland Health Campus," she said.

"If a stand-alone clinic proceeds, it is an initiative of the State Government and SJGHC has no involvement."

Mr Kelly told the hearing that while the department was still in negotiations over the clinic, he was confident its services would be available when the main hospital opened.

He said those restricted services would comprise about 250 cases out of the 29,000 in-patients expected at the hospital each year.

However, Opposition health spokesman Roger Cook said it had been eight months since the expressions of interest process started, and he doubted the clinic would be ready in time.

"The Government will end up footing the bill for this," he said.

"They never should have given this contract to a provider who couldn't offer everything."