Tens of thousands of people rallied across Australia calling for the abolition of the January 26 national holiday in protests showing a deep division over a festivity intended to celebrate the birth of modern Australia.

While Australia Day marks the anniversary of the 1788 arrival of the "First Fleet" of British ships at Sydney Cove, many indigenous Australians, who trace their lineage on the continent back 50,000 years, regard it as "Invasion Day".

"Today marks the start of colonisation and the start of the genocide," said Jayden Riley, 17, who was marching in Sydney on Saturday in a singlet in the black, yellow, and red colours of the Aboriginal flag.

"It is not about refusing to celebrate being Australian. This day represents more than just being Australian to our people. My Nan's stolen generation, for example, she was taken from her family and brainwashed to be a Catholic."

At a rally in Sydney stretched along more than half a dozen city blocks, about 5,000 protesters chanted, "Always was and always will be Aboriginal land" and "No pride in genocide."

Protests attended by several thousand people took place in Melbourne, Canberra and other Australian cities.

'Pain and suffering'

Prime Minister Scott Morrison's right-leaning government, which faces a general election due in May, opposes any change to the holiday.

Attending official celebrations and a citizenship ceremony in Canberra, Morrison said it is idealism and enlightenment, not cruelty and dispossession that have prevailed in the country.

"These great ideas are the foundation of our modern Australia, and they have transformed us into this most recent chapter of our great story - the one we write together," Morrison told crowds in the capital.

Australia's 700,000 or so indigenous people track near the bottom of its 25 million citizens in almost every economic and social indicator.

"This country stops for a horse race, it stops for an AFL (Australia Football League) grand final, it stops for the Queen's birthday and it stops for an Anzac service and we don't have ever a time where this country stands still to reflect on first peoples of this country and the pain and suffering we've endured since colonisation," Lidia Thorpe, an Aboriginal former member of parliament, was quoted as saying by the ABC News.