The prisoners had broken into the prison's armory and seized a number of weapons, including rifles, handguns and more than 200 bullets, Justice Minister Lou Ying-shay told reporters Thursday.
Warden Chen Shih-chih and the head of prison guards, Wang Shih-tsang, were found safe, according to the island's justice ministry. Officials said the six men turned their guns on themselves.
The incident at the prison in the southern city of Kaohsiung unfolded at around 4 p.m. local time on Wednesday when the men grabbed a guard and member of the prison staff, the justice ministry told CNN.
The six inmates all worked in the sewing factory and would have had access to scissors, the ministry said. The inmates pretended to be sick and went to the prison infirmary. While there, they grabbed the keys from prison staff but were unable to break out of the prison. They smashed their way into a room storing the prison's weapons instead.
The facility's deputy warden, Lai Chen-jung, and head of guards, Wang, then offered themselves as hostages in exchange for the two held captive. The inmates then allowed Warden Chen to take the place of his deputy.
Claims of mistreatment
The inmates, who were serving a range of sentences for crimes including murder, complained about their sentences, mistreatment at the jail, and the recent release of former President Chen Shui-bian on medical grounds, according to Taiwanese media reports. He was serving a 20-year sentence for corruption.
One of the hostage takers, identified by Taiwanese media as Cheng Li-te, a member of a notorious criminal gang, issued a statement at around 11 p.m., which was read on Taiwanese television by Wu Hsien-chang, head of the Taiwan's Corrections Agency.
In it, Cheng pleaded his innocence. "I didn't kill anyone but I have to serve 18 years in prison. I'm not the only innocent inmate here. Who can speak out for us?"
He then complained that their monthly allowance of NT$200 (around US$6) was not even enough to buy underwear, and that prison inmates were denied the same chance of medical parole as former President Chen.
The inmates demanded safe exit by car via a side door of the prison.
The prison itself was locked down and surrounded by armed police, according to Taiwanese media, while relatives of the inmates were brought in to to assist with negotiations to secure the release of the hostages.
Early on Thursday morning Deputy Justice Minister Chen Ming-tang reported that the hostages had been freed but that the six inmates had shot themselves.
Warden Chen described how the inmates treated the hostages well, and seemed in good spirits throughout the siege -- even toasting each other before shooting themselves. He said Cheng and one of the other prisoners made sure their co-conspirators were dead before they shot themselves in the head.
Chen Chun-hsiu, a senior prosecutor with the Kaohsiung District Prosecutors' Office, told reporters at a press conference Thursday that he spoke to Cheng during the standoff, and was told that he planned to end his own life. He added that he did not seem mentally stable.
He said Cheng and the other inmates decided to take hostages to break out of the prison because they feared spending the rest of their lives incarcerated otherwise.