The vaccine rollout has been changed up to 25 times already, according to the HSE Chief Executive Paul Reid.
Speaking at a briefing on Thursday, Mr Reid said that they “expect and hope” that the Johnson & Johnson vaccine will become available during quarter two.
Use of the vaccine was paused by its manufacturer this week amid concerns from US regulators over rare cases of blood clotting.
Ireland was due to receive more than 600,000 doses of the single-shot vaccine between April and June, meaning plans for the vaccine rollout had to be quickly redrawn.
While these problems were offset by news of an additional 545,000 doses of the Pfizer jab, health bosses are still hopeful the J&J inoculation will be approved for use by the European Medicines Agency (EMA) next week.
“All we know right now is that it has been withdrawn for now, paused, and we can build based on that,” Mr Reid said.
“What we would expect, and we will certainly hope that the Johnson and Johnson does come back within the quarter, with whatever definitions are defined by the EMA or NIAC (National Immunisation Advisory Committee) or the organisation themselves.”
However, the HSE’s latest modelling is based on the J&J vaccine not being made available this quarter.
Mr Reid told a briefing on Thursday that there are three variables that will determine the modelling for how many people can be vaccinated over the next three months.
These are the length of the delay on the J&J vaccine, the delivery schedule for the additional 545,000 Pfizer jabs and the possibility of extending the gap between first and second vaccine doses.
Mr Reid said the vaccine rollout had been changed up to 25 times already due to various issues, and is likely to change again.
He said there has already been “huge benefits” delivered by the vaccine programme.
“It’s reducing our hospitalisations, our sickness and our mortality” he added.
On Thursday, the HSE launched a new online portal where people can register for their vaccines. It is currently open to people aged between 65 and 69.
Mr Reid said there had been 18,000 registrations completed by lunchtime on Thursday, of which 95% were done through the portal.