The ACT Opposition has called for an independent inquiry to be established after an ACT Health Directorate employee was stood down for allegedly tampering with Canberra Hospital emergency department waiting time data.

Forensic auditors have been called into investigate after the staff member took responsibility for changes to data that improved the emergency department's performance figures.

An external review of all data collection and reporting systems at the hospital will also be commissioned.

Opposition Leader Zed Seselja says a fully independent investigation should be established, such as the Ombudsman's inquiry that had looked into manipulation of crime statistics in Victoria.

"We can't allow the Government to investigate itself , we can't allow the government to set the terms of reference into an inquiry into how it doctored information," Mr Seselja says.

"This is far too serious and we won't accept that the Government can just cover this up in the way that they have in the past.This should be done by a completely independent person with sufficient powers to get to the bottom of how this occurred."

Chief Minister and Health Minister Katy Gallagher says she was shocked to learn on Saturday that the statistics had been tampered with.

But Ms Gallagher says she was pleased patient care had not been compromised by what had occurred.

She says it was possible more inquiries could be launched into the affair.

"We've got a reputable audit firm coming in and doing an audit. I think we should. ... get that done and see what it says and that will provide us I think with a clearer view about whether we need anything to happen," Ms Gallagher says.

"Obviously the Auditor-General is there, there is nothing to stop the Auditor-General and coming in to do an audit if they want to."

Health Director-General Peggy Brown says the inaccurate reporting on statistics had been happening for more than 12 months, and could have started as far back as late 2010.

She would not speculate on what motivated the senior staff member to change statistics.

"I will note however, that there was no personal or financial gain for the individual. I think they have made a very serious error of judgment seeking to slightly enhance the performance data of the emergency department," she says.

"It has been a very misguided decision."

Dr Brown says the overall impact on data is small, but the full extent is not yet known. In national emergency access targets recorded under the new National Health Reform, the directorate believes the overall change is 2 per cent.