Acting Premier James Merlino said authorities had genomically linked the West Melbourne Delta cluster to a man in his 40s who arrived from Sri Lanka on May 8.
The man, from the Glen Eira area, tested positive the same day and was moved from the Novotel Ibis to the Holiday Inn "health hotel" on May 14 before being released on May 23.
His genomic sequence is a match to the second of the two families identified at the North Melbourne Primary School as part of the West Melbourne outbreak.
But authorities are still unsure how the virus was transmitted from the returned traveller to the infected family.
Victoria's Deputy Chief Health Officer Allen Cheng said there were four main theories, with some more likely than others.
The "most likely" scenarios are that the man transmitted the virus to a staff member en route to the health hotel or a fellow guest inside the facility before it spread into the community.
"At this stage, we have not identified any high-risk incidents or interactions with staff or residents that may provide a clue as to the link to this outbreak," Professor Cheng told reporters on Tuesday.
Acting Police and Emergency Services Minister Danny Pearson said all 24 flight passengers and a Skybus crew had returned negative tests.
Some 268 COVID-19 Quarantine Victoria staff worked at the Novotel Ibis on May 8 and 9, and 360 staff at the Holiday Inn.
They along with 12 residents housed on the same floor of the Novotel Ibis have tested negative.
"I can confirm that so far there is no reported or obvious breach of infection prevention control protocols or anything else that would indicate a transmission has happened inside the hotel," Mr Pearson said.
Mr Merlino said there had been 21 hotel quarantine breaches across the country since the start of the pandemic, including two in WA and one in SA in the past month.
"We all know that hotel quarantine cannot be made risk-free," he said.
"Hotels are built for tourists, not for managing infectious diseases."
He wanted to reassure Victorians that the revelation would not set back plans to ease restrictions for Melbourne and regional Victoria at 11.59pm on Thursday.
"Our contact tracing team has done exactly what we needed them to do," he said.
"They have found the cases, they have tracked them down and they have isolated them."
Some 22,814 Victorians were tested on Monday and 21,192 received a vaccine dose at state-run sites.