Court proceedings were briefly halted when Mr Chen complained of an injury
Taiwan's ex-President Chen Shui-bian, who faces corruption allegations, has been formally taken into custody.
Mr Chen, an independence activist and staunch critic of China, was taken to jail after his detention was approved by a court overnight.
It came at the end of a dramatic 24 hours, during which police led a defiant Mr Chen away in handcuffs.
Mr Chen, who stepped down in May, denies all the graft charges and claims they are politically motivated.
He has been taken to Tucheng prison in the suburbs of the capital, Taipei. He can now be held for up to four months, despite not yet having formally been charged.
Police have reportedly tightened security around the jail amid threats from his supporters.
The BBC's Cindy Sui in Taipei says the authorities want to avoid the type of demonstrations seen last week during a landmark visit by a high-ranking Chinese Communist official to Taiwan.
Mr Chen and his supporters - who see closer ties to Beijing as a threat to Taiwan's sovereignty - opposed that visit.
Court proceedings had to be suspended on Tuesday night, when Mr Chen said he needed hospital treatment after being pushed outside the court building.
He was returned to court for an overnight sitting after doctors found he had only a minor muscle tear.
Mr Chen is accused of money laundering and illegally using a special presidential fund.
But the outspoken nationalist accuses the new administration of persecuting him "as a sacrifice to appease China".
Mr Chen is an ardent supporter of Taiwanese independence, and a trenchant critic of President Ma Ying-jeou's Kuomintang (KMT) administration, which he accuses of pandering to China.
But China has termed accusations that his detention is a plot between Beijing and President Ma's administration "pure fabrication".
President Ma has also denied intervening in the case.
Mr Chen and his family have been mired in corruption allegations since 2006, when his son-in-law was charged with insider trading on the stock market and then jailed for seven years.
The charges have damaged the reputation of the main opposition Democratic Progressive Party (DPP), observers say, which may now face a rough ride in next year's local elections.
Taiwan has been ruled separately since the end of the Chinese civil war in 1949.
The defeated Kuomintang retreated to Taiwan to create a self-governing entity.
But Beijing sees the island as a breakaway province which should be reunified with the mainland, by force if necessary.