Police have been accused of using excessive force in Central to drag 511 protesters from an overnight sit-in that followed the July 1 democracy march.
Officers are also said to have deprived those arrested of their rights during the action.
The mass arrests were made early yesterday on Chater Road and outside the chief executive's office in Admiralty.
The Hong Kong Federation of Students, organiser of the Chater Road sit-in, said it was unnecessary for the police to haul protesters away by force, as the federation had promised to end the protest at 8am.
"The action was a success. It has opened the way for more civil disobedience," deputy secretary- general Chan Shu-fai said.
He said the alleged maltreatment of protesters had laid bare the police's lack of manpower and the force's lack of ability to handle larger scale civil disobedience actions.
Chan and other student leaders were arrested for unlawful assembly and for aiding and assisting an unlawful assembly.
Eric Lam Lap-chi, a Kwai Tsing district councillor, said officers grabbed him by the neck and twisted his wrists as they dragged him away at about 3am, leaving him with scratches and bruises.
By 10.30pm yesterday, all of those detained were released with 25 given bail and 486 given warnings.
None of those arrested had been charged so far, police said.
Protesters said they were made to wait hours at a temporary detention centre in Aberdeen before they were granted access to lawyers and were given refreshments.
Barrister and lawmaker Alan Leong Kah-kit said five lawyers entered the centre at a police college at Wong Chuk Hang at 4am and met 11 protesters two hours later.
When another nine lawyers went in at 8am, they had to wait five hours to meet protesters.
"They didn't respect the rights of the accused to see the lawyers as soon as possible," said Leong, who went to the centre much later.
"The police's treatment of the lawyers is problematic."
Legislator Helena Wong Pik-wan, a member of the Independent Police Complaints Council, said some of the arrested were not allowed to visit the toilet as they were told there were not enough officers to escort them.
But Secretary for Security Lai Tung-kwok denied any maltreatment of the protesters.
He said the police had followed normal procedures, but it took time to process such a large number of arrests.
Lai said it was necessary for police to make the arrests as the protesters had blocked major roads and disrupted order.
Inside the police college, Qing Lam, 30, spoke to a South China Morning Post reporter over the phone after 1pm.
Qing, who was arrested at Chater Road, later said she was still waiting to give a statement five hours after that phone call.
The centre appeared to be overwhelmed with protesters, she said, but police did not supply food or water until noon - over three hours after her arrest.
Hong Kong police arrest hundreds of demonstrators at Chater Rd sit-in
Additional reporting by Tony Cheung and Samuel Chan