He said he hopes the incident does not dent confidence in the health service, and pointed out that Ireland is regularly in the top three safest places in the world to have a baby.
Mr Reilly said he understands that is little consolation to the family.
The minister said he wants the inquiry to find out if there are any lessons that can be learned from the tragedy.
He said a balance needs to be struck between the urgency of getting the answers, and the care that must be taken to get to the truth.
"What I want for the family is that, as quickly as possible, they have certainty about the facts of what happened here," he said.
"And I want for the Irish people to be assured that they have the full facts also as to what happened here."
The terms of reference and the membership of the HSE inquiry team into the case of Ms Halappanavar may not be completed until after the weekend.
It is understood the HSE is looking for an international expert to agree to join the panel. This process may take several days.
Ms Halappanavar, 31, was 17 weeks pregnant when she died after suffering a miscarriage.
Her husband Praveen has alleged that doctors refused several requests for a medical termination because the foetus's heartbeat was present.
He also alleged the couple were told: "This is a Catholic country."
Necessary that people speak with accuracy
Taoiseach Enda Kenny said we should await the outcome of the Halappanavar investigation to determine the facts.
He said it was necessary that when people speak about the death of Savita, that they are speaking with accuracy.
He also confirmed that Tánaiste Eamon Gilmore is meeting the Indian Ambassador.
He said that differences in opinion are only that. And this is a matter that has divided Irish society for a great number of years.
He said that he would not be rushed into a situation by force of numbers on any side.
He said that it was an issue that had to be dealt with rationally, openly and truthfully.
Current guidelines 'reflect current legal position'
Medical Council President Prof Kieran Murphy has said that its current guidelines on abortion were decided in 2009 and reflect the current legal position.
Prof Murphy said the guidelines are as accessible and as straightforward as possible and had received a plain English recognition mark.
He said that if the legal position were to change on abortion, then the guidelines would also be revised.
Prof Murphy said the guidelines were prepared after extensive consultation with the public and the profession.
He was speaking outside of the annual conference of the Medical Council in Dublin before a debate on "the medical moral maize" and ethical guidance for doctors.
The Irish Patients' Association has said the review group to investigate the case of Ms Halappanavar must have a number of independent patient advocates on it.
IPA Chairman Stephen McMahon said he had received emails from India expressing anxiety and a perception that Ireland was in the dark ages.
He said the concerns needed to be dealt with professionally and by a thorough inquiry.
Ambassadors
The Department of Foreign Affairs has confirmed that Ireland's Ambassador to India is meeting Indian politicians and officials to try to ease concerns over the death of Ms Halappanavar.
The Indian Ambassador to Ireland has said he hopes that steps will be taken by the Government to ensure that nobody else dies in similar circumstances.
Speaking on RTÉ's Morning Ireland, Debashish Chakravarti said there is a lot of anguish among the Indian community in Ireland and in India about the death.
Mr Chakravarti said he has met government officials in Ireland and conveyed his concerns about her death.
He said he hopes that the investigation is carried out as quickly as possible without affecting the quality of the inquiry.
The ambassador said that abortion is not illegal in India when the mother's life is at risk and he said if the situation had happened in India he could not say what action the doctors would have taken.
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