'The blackest day'
The government said it was responding by giving the Australian Sports Anti-Doping Authority increased powers and resources to investigate the issues.
It also said that if "persons of interest" refuse to cooperate with the authority's investigations, they could face civil penalties.
"Don't underestimate how much we know," Clare said. "If you are involved in this, come forward before you get a knock at the door."
He added that as a result of the commission's report, authorities believe "multiple potential criminal offenses have been committed," and the relevant information has been passed onto police.
The catalog of problems exposed by the commission's report prompted expressions of dismay and disgust in Australia.
Richard Ings, a former head of the anti-doping authority, summed up the mood.
''This is not a black day in Australian sport, this is the blackest day in Australian sport," he told the Australian Broadcasting Corporation.
In an interview with CNN, Ings called the report a "wake-up call" for sports and suggested that other countries should take a look at their own sports programs to check for doping and corruption.
"What is happening here and what has been uncovered here could easily happen in any other jurisdiction and any other country around the world," he said.
Many prohibited substances in use nowadays cannot be detected by existing drug testing programs, according to Ings.
"The game has changed," he said. "It's now about investigations, it's about law enforcement, it's about exactly what happened with Lance Armstrong."