Given the rate of new cases across the world was close to 1 million per week, Professor Murphy said hotel quarantine remained essential.
Speaking after today's meeting of National Cabinet, he said testing of people in hotel quarantine would be ramped up.
But he also indicated that could lead to quarantine being changed in some circumstances.
"We're seeing imported cases in hotel quarantine from a different range of countries now," he said.
"We are going to start testing people on entry to quarantine and testing people before they leave quarantine to see whether a testing regimen might help in the future to modify that quarantine in certain circumstances."
All those in hotel quarantine will be tested within 48 hours of arriving and again on day 10 to 12 of their two-week stay.
But Murphy also implied people may be required to undertake tests while being kept in hotels.
- "The states have the powers … to say to someone well, we won't let you out of quarantine until you've been tested and had a clear test," he said. -
"I think most people, when they understand … that this is a requirement, I think most people will cooperate with that arrangement."
Prime Minister Scott Morrison said the decision on how to administer the tests would ultimately be up to the states.
"It is a matter for the states in terms of what's done within their borders, within their jurisdictions, in terms of complying with requests," he said.
IMAGE data - Days since the last reported case of COVID-19
NSW 0 VIC 0 QLD 1 WA 4 ACT 20 SA 32 TAS 43 NT 56
Last updated 19:06 PM AEST on Saturday, June 27
Mr Morrison said state and territory leaders had reaffirmed their support for the 14-day hotel quarantine program for at the National Cabinet meeting today.
This morning Victoria's Deputy Chief Health Officer said of the 18,000 people to have gone through hotel quarantine, 30 per cent had declined a test for the virus.