Many left as bailiffs and police removed the camp’s barricades but some vowed to stay despite police warnings.
Police began their operation early on December 11 in what is widely seen as the final act in the long-running protests.
The number of protesters has dwindled in recent weeks from the tens of thousands who turned out in September.
They want Beijing to allow free elections for the territory’s next leader in 2017. China says everyone can vote but a pro-Beijing committee will screen candidates.
Police officers started to clear the camp and dismantle tents after issuing orders for protesters to vacate the “occupied area” within 30 minutes or face arrest.
Among those reportedly arrested were opposition Democratic Party founder Martin Lee, student leader Nathan Law, media tycoon Jimmy Lai and singer Denise Ho.
As police approached the last remaining protesters, Alex Chow, head of the Hong Kong Federation of Students, rallied the crowds, saying the fight was not over, AP reports.
Meanwhile, a dozen people who opposed the protests turned up to cheer on the police, the South China Morning Post reports.
Earlier in the morning, bailiffs read out a final warning to protesters shortly before workers, backed by police, moved in and began dismantling barricades in one section of the site, using box cutters to remove ties.
Footage from the scene showed police tearing down supply and first aid tents, as well as a study area used by students.
Trucks with cranes were also used to pick up debris left behind from the broken barriers, plastic sheets and umbrellas.
The clearance is the result of a court order obtained by a bus company which says the protests have disrupted its business.
While the order covers three portions of the Admiralty site, including the main Connaught Road area, Hong Kong police spokesman Cheung Tak-keung said officers would also clear blocked roads.
He said they would clear away barricades from a second protest site at Causeway Bay site “at an appropriate time”. About 20 people remain there, the South China Morning Post reports.
Some pro-democracy politicians have joined the students at the site and academics and a police watchdog are monitoring the clearance operation.
Some protesters, however, packed up their tents as Thursday dawned.
Clashes erupted when a third protest site, at Mong Kok, was cleared last month.
On December 10, Hong Kong’s top civil servant Carrie Lam urged students to leave the Admiralty site peacefully.
Later that night, more than 10,000 people gathered at the protest site, chanting pro-democracy slogans in what many saw as a farewell to the current demonstrations.
At their height, the protests were seen as the biggest challenge to Beijing’s rule in Hong Kong since the 1997 handover.
Rallies in late September and early October saw huge crowds on the streets. But numbers fell as weeks passed and many Hong Kong residents also spoke out against the protests because of disruption to the city.
Beijing has not moved from its position on Hong Kong’s election process, describing the demonstrations as illegal.
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