Attempts to completely decriminalize abortion as part of the new legislation failed after the debate in Dáil.
A number of TDs called on Health Minister Harris to support amendments to the Decree on the Abolition of the Pregnancy Act, which would see doctors protect themselves from criminalization where they act in good faith and who would put down the current jail sentence of 14 years.
Independent TD Clare Daly said that the move to decriminalize abortion was one of the most important of the 65 amendments.
"We are here in an important situation and if we pass this legal regulation, but we hold the criminal sanction in it, I do not think we can succeed.
"We need to move away from linking abortion to 14 years in prison."
She said that the failure to remove criminal sanctions leaves a "cold factor" for doctors and could leave health services open to "malicious reporting".
People before profits TD Richard Boyd Barrett said that health workers are scared of prosecution.
"Doctors who want to ensure the health and well-being of women in pregnancy situations will now work under anxiety and fear that if they perform certain things, they will be guilty of a criminal offense and be subjected to a 14-year sentence. This is obviously unacceptable to me."
Mr Harris said he felt obliged to bring a similar law to what was presented to the people, and these provisions contained penalties and sanctions.
"I said after the referendum to get rid of the eighth, I felt the responsibility to stick to what was in the general scheme, and these provisions were in the general scheme," he said.
He said that Ireland is not alone on this issue, and in other countries the area is covered by laws with criminal laws.
The minister said that criminalization is necessary from the perspective of politics and to remove it can endanger the life or health of women. He pointed out that Bill would never face criminal sanctions on Bill himself.
He said that the provisions in the Bill would protect women who were forced to seek abortion or where there was a dominant personality or sexual abuse.
Fianna Fáil TD Billy Kelleher said that he was worried about the issue and that he wanted to be considered.
He agreed with Mr. Harris, however, that the government should not deviate from the proposed law that was presented before the referendum.
"You could have a vulnerable girl whose friend is helping or assisting with a tablet and could go terribly upside down. It's not good for a girl's health."
He said there were fears that, if she had presented it to a healthcare professional, her friend could be prosecuted or criminalized.
"When we look at this, we have to understand it from the practicality of what might happen. There must be some system." As I say in one breath, "I do not like deviation", I think we have to follow this to ensure that we do not discourage people from surrender to medical professionals if things go wrong, "Kelleher said.
Mr. Harris agreed that this issue should be "closely monitored" and that it could be part of a three-year review to be incorporated into legislation.
In connection with these amendments did not speak about anti-abortion TD.
Another amendment requiring public funds that are not used for abortion services was defeated in Dáil.
The request made by former Sinn Féin TD Carol Nolan was defeated by 90 votes for nine.
A discussion on the proposed three-day waiting period was also held. This is the period when a woman should wait before she could access the abortion medication. Independent TD Mick Wallace said he wants to drop a three-day wait in cases where this would lead to a woman unable to access a legal abortion for up to 12 weeks.
Solidarity TD Ruth Coppinger said that three days of waiting would affect ordinary women who would have to take more working days to visit the GP.
Fianna Fáil TD Mary Butler said that it is important that the government keep the three-day waiting period in the legislation, since that is what was before the referendum presented to the peoples of Ireland.
"Any proposal to remove this waiting would mean that the government deliberately deceived the public regarding the protective measures that would be in force. Many people voted on the government's guerrillas then. They have to keep their word," she said.