Dozens of mental health beds across South Australia are just weeks away from closing and 110 jobs are on the line as funding negotiations stall between the state and federal governments.

SA Mental Health Minister Leesa Vlahos said two national partnership funding agreements worth about $20 million would come to an end June.

Community-service provider, Neami National, will close more than 30 respite and in home beds next month.

SA Health is expected to close 20 community rehabilitation beds in Whyalla and Mount Gambier due to funding concerns.

Ms Vlahos said she was working to find the funds to continue a forensic facility that houses inmates found not guilty due to mental incompetence.

"Oakden is particularly important because it has forensic patients who are coming out of periods of intense supervision, and having a community step down facility to allow those people to come back into the community is very important," she said.

Funding uncertainty unfair, Minister says

Ms Vlahos said the State Government had been "trying to talk to the Federal Government about this for a number of months" but had no communication returned.

"I'm in a position where I'd like the Federal Government to come to the table to talk about the national partnership arrangement," she said.

"We cannot continue to absorb the cuts after the last two federal budgets. We are trying very hard to make a difference in the community."

Ms Vlahos said the uncertainty surrounding the funding was unfair on patients and staff.

"You cannot keep clinicians and qualified staff in these places on hold because they haven't decided yet or they've got a long-term budget strategy," she told 891 ABC.

Morris Corcoran, who inspects all acute mental health units in the state, said a funding cut would be foolhardy.

"If we have a log jam in an emergency department, it is a significant cost on a daily basis to have people with a mental health condition staying in an emergency ward," he said.

"The longer they're in there, the more likely it is they're going to become more unwell."

The ABC has sought the Federal Health Minister's response.