In Sydney, organisers said some 30 people were arrested, including four girls aged under 16.
"Alleged offences committed range from obstructing traffic to disobeying reasonable direction," NSW Police said in a statement.
Assistant Commissioner Mick Willing said police respected the right of groups and individuals to protest, but "we have a responsibility to the community and local businesses to ensure they can go about their normal activities without being impacted on or put at risk".
"Unfortunately, despite the warnings issued by local police and our colleagues from across the country, this group continue to set out to break the law and put themselves and others at risk," Mr Willing said in a statement.
Monday's rally saw hundreds of people march from Belmore Park to Sydney's CBD via Pitt St.
In Melbourne, protesters held a silent vigil on the steps of state parliament before marching through the city, blocking Flinders Street before being forcibly removed by police.
Participant Brad Homewood told SBS News "we're very much like a smoke alarm".
"People might get irritated when it goes off in the middle of the night, but they soon realise it's gone off for a good reason. It's there to wake them up and alert them of imminent danger."
He hoped Australians would "think of this movement in that context".
In Canberra, hundreds of people marched across Canberra's Commonwealth Bridge at the foot of Parliament House.
Participant Jill Moran said Australia faced a "pretty grim" future if nothing was done to stop global warming.
"It's not the type of future that I would want ... Causing disruptive action is really our only choice," she said.
A group of activists locked themselves to a bridge in Brisbane and in Tasmania, activists gathered at Cradle Mountain.
In the leadup to the events, Home Affairs Minister Peter Dutton suggested climate protesters should be publicly shamed and have their welfare payments cut off.
"A community expectation is that these people are heavily fined or jailed," he said.
Extinction Rebellion spokeswoman Jane Morton said the protests are the only way to urge governments to listen to experts and act on climate change.
"There's no alternative and we do apologise for the disruption because we believe it's the only way we can get our message out," she told 3AW on Monday.
"It's pressure and it's the only way we know to save my kids, your kids if you've got any."
New Zealand begins protests
The Global Extinction Rebellion protests started in New Zealand on Monday morning, where participants staged rallies and a CBD sit-in to support environmental protection.
Around 300 protesters were involved in the New Zealand action, centred on the Ministry of Business, Innovation and Employment (MBIE) headquarters.
Self-proclaimed "guerilla gran" Mary Rose, 80, travelled from Tauranga for the action, saying MBIE had been targeted for "its involvement in fossil fuel expansion".
"At one end of the street we've put a pink boat, the other end a pink car and around each are people that are locked on to block it off," she said.
Protesters glued their hands together and onto the MBIE building, forming a human chain to prevent employees from entering.
MBIE advised employees to work from home on Monday.
Other protesters rolled through the city with placards, banners and in costume.
Extinction Rebellion has started a worldwide campaign of civil disobedience in New Zealand
Another group travelled to the forecourt of New Zealand's parliament building, where a woman dressed in green breastfed a baby wearing an Extinction Rebellion beanie.
An Extinction Rebellion organiser said police had been "awesomely understanding", while a police spokesperson said there had been no arrests as of mid-morning.
The protest in Wellington's CBD was staged in a side street, away from major thoroughfares.
The protests come off the back of last month's School Strikes 4 Climate Action, a series of marches around the world inspired by teenage Swedish activist Greta Thunberg.
Around 150,000 people - or three per cent of New Zealanders - took part in those marches around the country.
Prime Minister Jacinda Ardern said that figure, believed to be the highest number of protesters per capita in the developed world, made her "proud".
But just like many of last month's marchers, Ms Ardern was sharply criticised by Extinction Rebellion activists.
Melanie Vaulter, who locked herself to the de-wheeled car at one end of Wellington's Stout Street, said Ms Ardern "said a lot of good things but we're yet to see much follow-through".
"They have good intentions and it gets watered down. We need much stronger action," she said.
"We need to de-carbonise. We live in a society built on fossil fuels and we live within political systems that perpetuate that."