Police detained around 400 people for offences including unlawful assembly and possession of offensive weapons, in the protest which organisers said more than a million people attended.
The police gave a far lower estimate of 60,000, a number the CHRF said was "too ridiculous".
In now-familiar scenes, riot police used pepper spray, tear gas and water cannon, while hardcore protesters lobbed petrol bombs, built makeshift barricades and vandalised property belonging to businesses they consider pro-Beijing, including Starbucks and banking giant HSBC.
Police said around 400 people were arrested for offences including "unlawful assembly and possession of offensive weapons".
The Wednesday clashes were, however, small compared with some of the chaos witnessed in the city in recent months.
The unrest in Hong Kong was sparked last year by a proposal to allow extraditions to mainland China. It has since morphed into a larger revolt against what many fear is Beijing's tightening control over the semi-autonomous city.
China and the Hong Kong administration have refused to accede to the protesters' demands, which include fully free elections in the city, an inquiry into alleged police misconduct, and amnesty for the nearly 7,000 people arrested during the movement, nearly a third of them under the age of 20.
At the new year rally today, #HongKong police officer pulled off the mask of a Legcp councillor and pepper sprayed him for no reason #PoliceState #PoliceTerrorism #HongKongProtests pic.twitter.com/RivfD3zxZe— Freedom HK (@FreedomHKG) January 1, 2020
"It is sad that our demands from 2019 need to be carried forward to 2020," the CHRF's Jimmy Sham said at the start of the rally.
Activists have accused the police of brutality and rights violations, while city authorities, and the central government in Beijing, have accused anti-Beijing protesters of rioting.
China has also alleged that the unrest has been fanned by foreign powers, and has bristled at criticism from rights groups and governments of the way the protests have been handled so far.
Hong Kong saw in the new year with an evening of peaceful protests that descended into tear gas-choked clashes between hardcore demonstrators and the police overnight.
The protest movement has become quieter since the city's anti-Beijing camp scored a landslide victory in a municipal-level vote in November seen as a referendum on the Beijing-backed government and violent clashes at some of the city's university campuses.
But protesters have vowed to continue their fight for greater freedoms.
"Hong Kong people have been pushed to a hopeless situation. That's why today we have to come out," a masked protester said in a speech at the rally on Wednesday.
The unrest that began in June last year is the biggest crisis the former British colony has faced since its return to Chinese rule in 1997.
There have been at least two protest-linked deaths since the beginning of the unrest, and around 2,600 injuries.
Under the terms of the 1997 handover, Hong Kong enjoys unique freedoms unseen on the mainland, but fears have increased in recent years that they are being chipped away as Beijing exerts more control over the territory.
This is how Hong Kong spent New Years Day.— Joshua Potash (@JoshuaPotash) January 1, 2020
1 million protesting in the streets.
It’s also how they spent Christmas Eve. And Christmas Day.
Incredible and inspirational dedication.
A huge New Year's Day anti-Beijing rally in Hong Kong ended in mass arrests and clashes between police and hardcore protesters, as demonstrators sought to carry their movement's momentum into 2020.
Hong Kong has been battered by nearly seven months of unrest, its biggest political crisis in decades, which has seen millions come out on the streets demanding greater democratic freedoms.
Organisers claimed more than a million people gathered for Wednesday's rally, which had approval from the authorities, and marched across the international financial hub's main island in an attempt to put pressure on the government to meet their demands.
But after a peaceful start, violence erupted near the march within hours, with police and masked protesters facing off in several neighbourhoods on the city's main island.
The Civil Human Rights Front, the umbrella group which organised the march, said authorities ordered them to end it after the clashes began.
"We believe the total turnout for today's march has surpassed the 1.03 million on June 9," the group announced, referring to the massive rally last year that kicked off the protest movement in earnest.