The state's hotel quarantine program has failed to prevent the spread of coronavirus, and is instead central to the rising case numbers.

The Accommodation Association said the government needs to own up to its failings, fix the mess and apologise to hotels helping it out.

"These hotels stepped up to do their duty and then to be absolutely cast out to sea the way that they have by this government is really disappointing, it undermines the confidence in the relationships we've built," AA CEO Dean Long told AAP on Friday.

"We trusted the government to run a good program and that appears not to be the case."

Mr Long said the accommodation industry did not manage these sites, instead that fell to the state government.

"This is effectively an example of a failure of process ... and it is leading to a failure of leadership," he said.

"These sites in the city have been nationalised, turned over to the government who have appointed the staff and the processes, and then to blame an industry for the government's own failure is disturbing."

The program has become such a thorn in the government's side that a judicial inquiry into the program was announced on Thursday.

Hotels under scrutiny such as Rydges on Swanston and the Stamford Plaza Hotel said that they did not hire the security staff.

"Rydges on Swanston has had no involvement in the hiring of security personnel and is fully supportive of the Judicial Inquiry into the Hotel Quarantine Program," Rydges Hotel's Troy Cuthbertson said on Friday.

While Stamford Plaza Hotel said it "had not breached any infection control protocols", and had merely been accommodating returned Australian citizens at the request of the state government.

It confirmed that a security contractor, hired by the state government, tested positive on or about June 13 and none of its staff have the virus.

The state's tourism industry has had "the worst year on record" after the summer's bushfires and now COVID-19, Mr Long added.

Australian Associated Press