President of the Australian Medical Association Tony Bartone urged all protesters to stay home, monitor their health and get a coronavirus test if they develop any symptoms.
"No matter how much hand sanitiser, no matter much the masks were being worn, for those periods of time there is a risk of the virus passing," he told 3AW.
“If everyone was wanting to keep the rest of the community safe, anyone who attended those rallies really should stay home and keep away from the rest of the community for at least two weeks."
Deputy Chief Medical Officer Nick Coatsworth said he understood the AMA's call for people to self-isolate, but it would be difficult to enforce.
"There would be challenges and implement in such a policy and I would say to protesters who may be concerned, that they simply follow what their state and territory health departments recommend," he said.
"I fully endorse the AMA's president's statement people with symptoms get themselves tested, that is absolutely critical," he added.
Senior government minister Simon Birmingham described the timing of Black Lives Matter marches as "incredibly unfortunate", but acknowledged it was not of the protesters' choosing.
There are fears the nationwide protests, which were also focused on indigenous prison rates and deaths in custody, could trigger a spike in coronavirus infections.
Sydney Black Lives Matter protest goes ahead
"I think the timing was incredibly unfortunate and I accept events that occurred in the United States were not within the control of any of the protest organisers," Senator Birmingham told ABC radio on Monday.
"Nonetheless, there could have been other ways of trying to create the type of movement and symbolism the protesters sought without having to resort to mass gatherings."
Senator Birmingham suggested alternatives like the driveway commemorations on Anzac Day.
"There are different ways of activating mass community sentiment without it requiring mass gatherings," he said.
Senator Birmingham said he understood the sentiments of the protests, but argued it showed a lack of regard for other Australians who made sacrifices during coronavirus lockdowns.
Meanwhile, Labor's indigenous affairs spokesman Pat Dodson said it was not responsible to describe protesters as uncaring.
"Unless there's a voice to the parliament that can express clearly the compassion and concerns Aboriginal people have got over the predicaments they face on many fronts, then you're going to have people defying the odds to try and at least get their point of view across," Senator Dodson told ABC radio.
"That can be a great risk to themselves as to others."
Australia's chief health officers are meeting on Monday to discuss the next step in easing coronavirus restrictions.
Deputy Chief Medical Officer Paul Kelly said the mass rallies would be taken into account.
"At the moment, it won't change how we are viewing those processes, but in particular states it may do, depending what happens in relation to any cases that crop up," he told reporters on Sunday.
There have been 7260 confirmed cases of COVID-19 in Australia and 102 deaths. More than 1.6 million tests have been conducted across the country.
Activists speak at Melbourne Black Lives Matter protest
People in Australia must stay at least 1.5 metres away from others. Check your state’s restrictions on gathering limits.
Testing for coronavirus is now widely available across Australia. If you are experiencing cold or flu symptoms, arrange a test by calling your doctor or contact the Coronavirus Health Information Hotline on 1800 020 080.
The federal government's coronavirus tracing app COVIDSafe is available for download from your phone's app store.
SBS is committed to informing Australia’s diverse communities about the latest COVID-19 developments. News and information is available in 63 languages at sbs.com.au/coronavirus