A Main Roads' officer's failure to pass on safety concerns relating to a flashing billboard on the Kwinana Freeway was an internal "error of judgement", the head of the agency has conceded.

The billboard, installed on a bridge overlooking the Kwinana Freeway at Bull Creek, was switched off less than a week after it was launched following a public backlash over safety concerns.

The State Government has confirmed it is responsible for the $680,000 construction cost of the sign.

Main Roads WA commissioner and Department of Transport director-general Reece Waldock yesterday admitted an external report prepared for the Main Roads prior to the billboard's approval raised safety concerns.

But he said he had not been made aware of its existence.

"Main Roads were there to again make an informed judgement about the safety," he said.

"They took advice and the advice came from two separate reports.

"One of the reports which weren't brought to my attention or the managing director's indicated some issues."

He said the reports were prepared externally.

Labor MP Ken Travers asked Mr Waldock during a budget estimates hearing yesterday why the report was not used in approval processes.

"How was that report not brought to the attention of the decision makers prior to decision being made to approve that sign at that location?" Mr Travers said.

"It was held at an officer level and wasn't, it wasn't put through the system."

Government accused of cover-up

Mr Waldock said the decision was an error of judgement on the part of a Main Roads officer.

"It was not provided up the line," Mr Waldock said.

Mr Travers has accused the Government of a "cover-up" for not releasing details of the report sooner.

"I think it's amazing that the department seemed to miss that advice prior to approving it, but more importantly that it's has taken so long to finally get the Government to concede that they had received a report that raised safety concerns prior to approving it," he said.

"I think there has been a cover-up going on here but we have finally got the truth [to] come out.

"I think people could not believe that that sign would have been approved in that location, there have been numerous parliamentary questions, media inquires and it has taken to till now."

Mr Travers said he has requested the report be released.

"I think it raises very serious questions about the internal operations of the agency, and I think the fact that the Government has been so slow to admit that this report even existed says that there was more to this issue and that we'll need to continue to keep digging," he said.

Transport Minister Dean Nalder said as soon as he was made aware of a safety audit concerning the billboard, he asked the Public Transport Authority to turn it off pending a full investigation.

"I understand that MRWA is still conducting that investigation and compiling advice for my consideration," he said.

"I will not give authorisation for that billboard or any other billboard to be installed or switched on until I am fully satisfied that the safety concerns raised in any report or audit can be remedied."