Manager Pat McLaren has resigned after the Department of Health Human Services (DHHS) investigation.

Ms McLaren resigned last week and has been replaced by an interim manager. 

The service will continue to provide domestic violence support services. One of the issues was a bullying and harassment complaint by a staff member against Ms McLaren that was then referred by the Emma House board back to Ms McLaren for investigation.

It is expected the board will be restructured.

A DHHS spokesman said the department's local office had contacted the agency to discuss the outcome of the report with senior management and the board for a prompt implementation.

"This will ensure the continued delivery of quality family violence services in the south-west of Victoria," he said. 

The spokesman confirmed that one senior staff member had resigned from Emma House.

Former Emma House board member Bernadette Northeast raised governance issues with DHHS and hoped the organisation was now in a better position to deliver family violence services.

"The reason I left was due to governance and management issues and my inability to improve things,” she said.

“I hope the service can now move forward.

"The board previously did not have the capacity or skills to govern Emma House.”

Ms McLaren could not be contacted for comment.

Emma House chair Deb Nicholson said the service had been happy to work with DHHS.

She said Emma House was now in a good position to respond to upcoming changes brought about by the Royal Commission into domestic violence.

Ms Nicholson said she never doubted Emma House's ability to deliver quality services to "thousands of women and children across the south-west".

A DHHS spokesman said that following concerns raised last year regarding management and governance at Emma House, the department initiated an independent review, with the recommendations currently being implemented.

He said the department was working with Emma House’s board to fix issues identified in the investigation. "Emma House has appointed an interim manager for three months. The department continues to have confidence in Emma House delivering services to women and children," he said.