Health Minister Stephen Donnelly has said a new vaccine roll-out plan will be produced "very shortly".
The news comes as a second blow to Ireland's vaccination plan was announced as Johnston & Johnson said it is pausing its European roll-out after concerns were flagged in the US over blood clots. The news comes just one day after the roll-out of the AstraZeneca vaccine was limited to the over-60s.
Ireland is expecting 600,000 doses before the end of June from Johnson & Johnson.
The Food and Drug Administration (FDA) and the Centres for Disease Control (CDC) in the US have called for the immediate pause in the use of the vaccines after it emerged six recipients in the US developed a rare disorder involving blood clots.
This afternoon, Johnson & Johnson said it had reviewed the cases with European health authorities and decided to proactively delay the rollout of the vaccine in Europe.
This evening, Stephen Donnelly said: "I'm working very closely obviously with the department, the task force, the HSE all day today, late tonight, late last night and we're looking to have a new plan or an updated plan very shortly."
He added that calling the news "'a logistical headache' "would be certainly an understatement".
"If it follows through that there are restrictions, there's no question but that would require serious reprofiling of the programme," he said.
"However, it is important to say that the European Medicines Agency at this point has said they are aware of six cases in the United States out of nearly seven million vaccines that have been distributed.
"We've been here before, we've had quite significant changes from NIAC in the past and everyone involved has stepped up to reprofile the system and, critically, to keep the vaccines going out because we need to keep the pace of the vaccine programme, but what we're dealing with now is two things at once.
The Minister added that people with underlying conditions will hear this week what vaccine they will receive.
"I'm very, very aware that people are very much looking forward to getting this vaccine, particularly people in the very high risk group as a lot of them have really had to isolate themselves, lock themselves away for a whole year.
"It's incumbent upon us to move very quickly so later this week we will have a reprofiled programme and we'll be able to tell all of these groups of people when they can expect to be contacted.
"Johnson & Johnson is a big part of the programme, not this month, the volumes are pretty low, but by the time you get to June, it's several hundred thousand and it's a really useful vaccine as it's a single dose."
In a statement issued earlier today, Johnson & Johnson said the decision to pause the use of their vaccine was made out of an abundance of caution.
Ireland was due to receive 14,000 doses of the single-shot vaccine this week.
Earlier, it emerged that six women between the ages of 18 and 48 had developed a rare disorder involving blood clots. One of the women died and a second is in critical condition.
According to latest data, 6.8 million doses of the Johnson & Johnson vaccine had been administered in the US up to April 12.
In a joint statement today, Dr Anne Schuchat, Principal Deputy Director of the CDC and Dr Peter Marks from the FDA said: "We are recommending a pause in the use of this vaccine out of an abundance of caution".
They said it is important the health care provider community is aware of the potential for these adverse events so they can plan for proper recognition and management.
Treatment of this specific type of blood clot is different from the treatment that might typically be administered. Usually, an anticoagulant drug called heparin is used to treat blood clots.
In this setting, administration of heparin may be dangerous, and alternative treatments need to be given.
"Right now, these adverse events appear to be extremely rare. Covid-19 vaccine safety is a top priority for the federal government, and we take all reports of health problems following Covid-19 vaccination very seriously.
"People who have received the J&J vaccine who develop severe headache, abdominal pain, leg pain, or shortness of breath within three weeks after vaccination should contact their health care provider."
A meeting of the Advisory Committee on Immunization Practices is to be convened in the US tomorrow to further review the reported cases and assess their potential significance. The FDA will review that analysis as it also investigates these cases.
Health officials advised people who have received the Johnson & Johnson vaccine who develop severe headache, abdominal pain, leg pain, or shortness of breath within three weeks after vaccination to contact their health care provider.
Following the announcement, the Deputy CMO said that the European Medicines Agency is aware of US concerns over the Johnson & Johnson vaccine.
Dr Ronan Glynn was speaking to the Oireachtas Health Committee this afternoon and said that he would engage with the EMA in the coming days on the vaccine, which has yet to arrive in Ireland.
Meanwhile, a further 358 cases of Covid-19 have been confirmed by the Department of Health today.
The latest cases come as 18 Covid-related fatalities were identified.
Of the deaths reported today, seven occurred in April, three occurred in March, three occurred in February, and three occurred in January.