The deputy justice minister said the brutality of the men's crimes meant there was no reason to show mercy.
Campaigning human rights group Amnesty International has condemned the move as "cold-blooded killing".
The executions - by shooting -  "made a mockery of the authorities' stated commitment to abolish the death penalty", Amnesty said in a statement.
"It is abhorrent to justify taking someone's life because prisons are overcrowded or the public's alleged support for the death penalty," the statement said.
The executions were carried out in three separate prisons in different parts of the country - two in the capital, Taipei, two  in the central city of Taichung and two in the south of the island.
All six of the men had been convicted of murder.
The BBC's Cindy Sui, in Taipei, says the executions come at a time of inflamed public debate about the death penalty following the death of a boy in a video arcade.
Local media reported the 29-year-old suspect had said he would get life in prison at most "even if he were to kill two or three".
He also reportedly said he would get free room and board in prison.
The reports led to public calls for all of those on death row to be executed.
A spokeswoman for the ministry of justice said that the executions had been carried out on a Friday evening to avoid a strong public reaction.
Though religious and human rights groups oppose capital punishment, most victims' families are in favour, and surveys suggest that most of the population also support the death penalty.
The ministry said it has the obligation to carry out the law until there is public consensus on abolishing the death penalty.
According to the state-run Central News Agency, there are a total of 55 death row inmates following the executions.
Taiwan executed five prisoners in March 2011 and four in April 2010.
The 2010 executions were the first after a hiatus that had lasted since 2005, when it adopted an informal moratorium on the death penalty.
Taiwan has executed six death row inmates, the first use of the death penalty this year.