Mr Harris spoke about the sheer panic and desperation the families must have felt as news of the fire spread on that fateful night in 1981.
"Being accused of telling lies, the smear of arson attached to their loved ones, having their grief and sadness misconstrued as madness, a sense of threat and suppression when they simply started looking for answers", he told the Dáil.
He also added, "Stigma heaped upon sorrow breed shame and silence".
Taoiseach Harris also stated that it is to "our great and eternal shame that far from the warm embrace of a caring state, the Stardust families experienced a cold shoulder, a deaf ear and two generations of struggle for truth and justice".
He added that the "state processes heaped misery on tragedy".
"I am so deeply sorry that your first bid for justice ended with suspicion being cast on those who had died or survived on that catastrophic night", the Taoiseach continued.
He also said that the "terrible reality is that we will never know for certain how many lives were ended by this tragedy".
"Beyond the 48 whose names we know, there were countless others whose lives were turned to ash on that terrible night," he continued. "Their hopes and dreams were destroyed twice over".
"First by the fire, and then by the successive failures of the State to do what was right", he also added. "And for that I am truly sorry".
Taoiseach Simon Harris also signalled out three women who were made to wait in a "cold hut", when they visited Government Buildings 15 years ago.
Mr Harris also praised the "indomitable spirit in refusing to be kept out in the cold" of Gertrude Barrett, Antoinette Keegan, and Bridget McDermott who have "led us to this moment today.
He also added, "The fourth woman who was there, Christine Keegan, and her late husband, John, didn't live to see this day".
Quoting Christine's words from a statement that she had prepared for this inquest, Mr Harris also stated this.
"The Stardust fire took all our happy family days away from us, it took away all our belief in faith and it took away our trust with successive governments over the years", he said.
"We felt abandoned and all alone and left like lambs to a slaughter, everything brushed under the carpet, to keep the truth hidden".
"I would like to ask a question to the Government, the establishment, and its agencies", he continued.
"What did we families of the deceased victims of the Stardust fire ever do on the government, to deserve this ill treatment and constant systematic abuse we have sustained for the past 38 years?".
Simon Harris also said that he intends to answer this question.
"You did nothing wrong," he insisted. "The institutions of the State let you down".
"These brave families should never have had to walk alone. We should have been by your side, walking with you. We were not. And for that we are truly sorry".
