A health professional says the Ministry of Health's fractured relationship with the Canterbury District Health Board will take some hard work to repair.

Relations soured on Friday after CDHB specialist Geoff Shaw's complaint against National Health Board acting director Michael Hundleby was thrown out.

Earlier, Shaw's complaint was forwarded by the DHB to the Ministry of Health. They commissioned Dundas Street Employment Lawyers to conduct the investigation - a firm that had previously done work for the Ministry.

The case was thrown out due to unsubstantiated claims.

Association of Salaried Medical Specialists Director Ian Powell said the health ministry faces an uphill battle.

"They've really got to work very hard on improving their relationship with senior doctors employed by the Canterbury DHB and their managers as well."

"It's a pretty sorry state" he added.

Powell believes the complaint needs to be revisited.

"It should actually go back to step one and have an independent investigation into the complaint made by Professor Geoff Shaw concerning a senior Ministry of Health official."