Six people were arrested on Friday for offences ranging from forcibly entering government property and public disorder to assaulting an officer, police said in a statement.
Around 150 people pushed into the grounds of the complex, some scaling over a tall exterior fence, as others outside yelled "open the gates".
Police repeatedly used pepper spray on the protesters, who used umbrellas, surgical masks and goggles to protect themselves, an AFP reporter at the scene said.
Officers held up red signs warning people to "stop charging or we use force". Riot police wearing helmets and carrying shields arrived to push back the crowd in the early hours of Saturday morning.
Student groups are spearheading a civil disobedience campaign along with democracy activists in a days-long protest at Beijing's announcement last month that it would vet who can stand for Hong Kong's top post of chief executive at the next election.
By early Saturday, around 1,000 people were outside the Southern Chinese city's main government complex. Numbers had earlier swelled to more than 2,000 as secondary school pupils, some wearing uniforms, joined the university students.
In a statement police confirmed they had made six arrests of Hong Kong citizens aged 16 to 29, and that around 150 students had entered the government grounds. News footage showed officers taking away prominent student leader, Joshua Wong.
Early Saturday, a government statement had "expressed regret" that protesters had stormed the complex, saying security personnel, police officers and protesters had suffered injuries but without giving details.
"We don't care if we get hurt, we don't care if we get arrested, what we care about is getting real democracy," protester Wong Kai-keung said from the front line of the charge.
Chung Chun-wai, 17, said many of his friends joined the protest in defiance of their parents, highlighting the often sharp generational divide in the former British colony over its political future.
"I think secondary school students are a part of society and I consider myself a citizen of Hong Kong. That's why I think I need to bear the responsibility to care about society and to voice the real opinions of Hong Kongers," he said.
Occupy Central, a prominent grassroots pro-democracy group, has vowed to take over the city's Central financial district if its demand that Hong Kongers be allowed to nominate who can stand for leader is not met.
Last month China said Hong Kongers would be allowed to vote for their leader for the first time in 2017, but that only two or three candidates approved by a pro-Beijing committee could stand.
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