They were silently marking the birthday of Falun Gong founder, Li Hongzhi, who lives in exile in the United States.
Witnesses said some followers were kicked and beaten by police as they were detained.
The Chinese Government outlawed Falun Gong last July after branding it an "evil cult". Members say thousands of practitioners have been rounded up since the ban.
Kicking
Followers arrived in Tiananmen Square early in the morning and began meditating in small groups.
Witnesses said demonstrators managed to unfurl large banners bearing the name of their movement before they were arrested.
Many were middle-aged women who got quietly into the police vans after being detained.
But reports said one man endured kicking, beating and slapping by plainclothes police as he shouted: "I am practising Falun Gong. What can you do to me?"
Police also forced tourists with cameras to expose their film, and one with a video camera was detained.
Crackdown
Falun Gong, which claimed tens of millions of followers in China before it was outlawed, combines traditional Chinese breathing exercises with Buddhist and Taoist philosophies.
In recent months, practitioners have flocked to Tiananmen Square to protest against the ban.
The nationwide crackdown was sparked in April last year after 10,000 followers gathered in Beijing in a silent protest against official harassment.
Key leaders of the group have since been sentenced to up to 18 years in prison.
Earlier this week the authorities said they had accomplished a decisive victory over the movement and that 98% of its followers had recanted.
Protests
In Hong Kong, the only part of China where Falun Gong is not banned, practitioners staged a parade to celebrate Mr Li's birthday.
The Falun Gong movement in New York said the organisation was planning events in 120 cities in 30 countries to mark World Falun Dafa Day on Saturday.
Thursday's protests marked the 48th birthday of Mr Li who has not been seen in public since China banned the movement and put him on its most wanted list.
Victory
Beijing's crackdown has been strongly criticised by Western governments and human rights groups.
But China's state media marked the day with a lengthy commentary declaring a "decisive victory" over Falun Gong.
"This is an important political struggle affecting the country's future and fate and a great dissemination of the scientific Marxist world view," said Xinhua news agency.
"This victory has fundamentally smashed the evil cult organisation of Falun Gong and isolated a small number of hard-liners headed by Li Hongzhi."