Calvary Public Hospital's performance and financial management and data collected by ACT Health will be reviewed by the ACT Auditor-General, it was announced on Thursday.
The two new performance audits will be completed along with already announced audit work in the 2015-16 financial year and will be finalised within months, Auditor-General Maxine Cooper said.
The audits come as the government has faced repeated criticism over hospital management and data errors inside the health directorate, as well as reports of bullying and mismanagement at the Canberra Hospital including the obstetrics and gynaecology unit.
In 2012 the government faced allegations of "data doctoring" in territory health services after it was revealed patients records had been manipulated to improve reporting outcomes.
Providing nearly 30 per cent of the territory's public hospital service, Calvary received $166.73 million from the government in 2013-14. The audit will consider the factors that contributed to incorrect financial information being provided to the government by Little Company of Mary Health Care and Calvary Health Care.
A hospital spokesman declined to comment.
Dr Cooper said the audits would use new "follow the dollar" powers for the first time, whereby non-public entities can be audited because they receive taxpayer money.
The effectiveness of contracts with the hospital, governance, financial and performance management issues will also be considered as well as the integrity of activity funding data reported by Health to the Independent Hospital Pricing Authority and the effectiveness of Health's management of the data.
"It is important for the community to have confidence in how ACT Health funds are managed and focusing on arrangements with Calvary Public Hospital is prudent given its significant role in providing public hospital services," Dr Cooper said.
Last year Calvary's budget black hole was found to be more than double initial calculations, as documents showed an $11.3 million loss.
The hospital had to withdraw and then reissue its 2013-14 financial report with ASIC after re-examining records to ensure they complied with accounting standards.
Calvary Health Care ACT warned it could seek a bail out from its parent entity and a staffing freeze was implemented.
In January, it was reported an audit of ACT Health had uncovered potential violations of privacy and processing errors as well a mystery $5.2 million debt to Calvary, which turned out never to exist.
The Audit Office gave ACT Health an unqualified outcome, but found a large number of problems throughout the directorate which could have led to fraud and corruption.
Opposition Leader Jeremy Hanson welcomed the announcement of the audits on Monday.
"There's no question there have been issues within ACT Health and I think everyone would be aware of the fabrication of data on a massive scale in 2012... so the fact the Auditor-General will investigate data integrity is welcome," he said.
"I think by virtue of the Auditor-General looking at these areas, to some extent, reflects the concerns that a number of people have. I think it is important in restoring confidence in ACT Health data that this process is completed."
A spokesman for Health Minister Simon Corbell confirmed the government was aware of the announcements "and will assist the auditor as is required".
"The Auditor General consults with government about the audit program," the spokesman said.
A spokeswoman for ACT Health said it would "co-operate and work closely with the ACT Auditor-General's office throughout the duration of the audits".