“We failed you when you needed us the most, from the very beginning we should have stood with you but instead we forced you to stand against us,” said Mr Harris.
The Irish premier has apologised on behalf of the state over the 1981 Stardust nightclub fire in which 48 people died.
A decades-long fight for justice culminated last week in an inquest finding that they had all been unlawfully killed in the Dublin tragedy.
Taoiseach Simon Harris said the state had failed families when “you needed us most” – and politicians stood in applause in parliament to acknowledge family members in the public gallery.
“I know you were forced to endure a living nightmare which began when your loved ones were snatched from you in a devastating fire,” Mr Harris said.
“I am deeply sorry you were made to fight for so long that they went to their graves never knowing the truth,” he added.
“Today we say formally and without any equivocation, we are sorry.
“We failed you when you needed us the most, from the very beginning we should have stood with you but instead we forced you to stand against us.”
Mr Harris said he hoped the inquest finding and Tuesday’s apology could help “end the neglect of 43 years waiting and fighting for the only thing you ever wanted, the truth”.
The taoiseach also met more than 70 people affected by the fire on Saturday to apologise.
The inquest ruling came after a previous finding, issued in 1982, said the fire was a result of probable arson – which the families never accepted.
That ruling was dismissed in 2009, leading to the latest inquest.
The fire took place in the early hours of Valentine’s Day when the Stardust nightclub, in Artane, north Dublin, was packed with 800 people. More than 200 were injured.
The fire started because of an electrical fault in an airing cupboard, the jury ruled.
In the main ballroom, foam in seating, the height of an alcove ceiling and carpet tiles on walls all contributed to the spread of the blaze, the jurors found.