NSW Waratahs coach Michael Cheika says the system of trust over the Australian Rugby Union’s medical protocols has been jeopardised after Israel Folau was ruled out of Saturday night’s Super Rugby match in Perth.

Cheika said he copped a gobful from a disappointed Folau following the ARU’s decision on the eve of the match against the Western Force.

The ARU’s chief medical officer Dr Warren McDonald made the decision late on Friday after getting specialist advice on the throat injury that kept the fullback out of the Waratahs’ last two matches in South Africa.

Cheika said the ARU had now twice broken their protocols with the Super Rugby franchises by seeking advice on Folau’s condition without first going through Waratahs team doctor Sharron Flahive.

“The whole system is predicated on trust, there’s certain jeopardy around that now,” Cheika told AAP on the phone from Perth on Saturday.

Cheika stressed that Folau had gone through all required medical tests over the past week.

“We’ve got a very experienced doctor who has seen this injury before,” Cheika said.

“We’ve put ourselves in the picture with lots of information. It’s not black and white, it’s not like having a broken leg.

“We’ve also considered the player and I think this is the biggest thing.

“We’ve been in contact with Israel every day. Last week we didn’t feel he was ready so we didn’t play him.

“This week he went through all the full contact training. He would have had more contact training on Tuesday than he would have in a game.”

“We went through all the tests that were required and I can tell you that no one from the ARU medical staff has spoken to Israel at all, which you have to think is a bit of a pre-requisite.

“I had to deal with him last night giving me a gobful because he’s not playing. I didn’t put him out.

“He’s a very smart guy – he understands what his body can do and where he’s at.

“From what I’ve heard from him, he’s very very disappointed with the way it’s gone down.”

Asked if he thought the NSW Rugby Union would formally protest to the ARU about their handling of the situation, Cheika said: “I’d say that we just do it out of process… I don’t think it’s going to make any difference.”

With Folau out, Cheika has shifted Kurtley Beale to fullback from inside centre, with Jono Lance restored to No.12.