The sentences were carried out late Friday, a day after Justice Minister Tseng Yung-fu signed the execution orders, a government statement said.
The six men who were executed had been convicted of "grave offenses" such as fatal kidnappings and multiple murders and were executed because of the brutality of their crimes, the statement said.
Their sentences were confirmed by court authorities at various levels, and the executions were carried out simultaneously in four prisons across the island, officials said, without saying how the executions were carried out.
The last executions in Taiwan were in March 2011, when five men were put to death.
Authorities in Taiwan have used extreme caution in carrying out executions amid growing pressure from local and international groups for the island to abolish the death penalty.
But the brutal murder of a boy at a video arcade this month triggered a public uproar and sparked renewed calls for tougher measures to curb violent crime.
A 29-year-old jobless man was arrested and charged with the boy's murder, and reportedly said later, "If you were to kill one or two persons, you will not be put to death," but you can have free meals in prison.
Lin Hsin-yi, an official with an alliance working to
But Wang Chien-hsuen, head of the government watchdog Control Yuan, said Taiwan should keep capital punishment to maintain justice and public safety.
"Many people have advocated abolishment of capital punishment to follow the international trend, but we should have our own standards," Wang said.
In a statement, human rights group Amnesty International condemned Taiwan's government for "credibly claiming it wants to see an end to the death penalty when it continues to conduct such actions."