HSE chief Paul Reid has said he is disappointed that family of staff in two hospitals received the vaccine ahead of frontline workers.
He said that such stories are not doing the programme any good.
Speaking on Today with Claire Byrne this morning, Mr Reid said while the stories relate to a small number of cases, he appreciates that it has caused significant distress among the public.
He said that the plan for sequencing was in place from the start and it was clear in terms of prioritising frontline healthcare workers.
"I don't think anybody needed further guidelines in terms of being clear about what work first should be done, what was the priority - it was made very clear in the sequencing document from the very start."
Despite the clear guidelines already in place, a further document was issued on January 12 which set out clearer principles and further detail on micro-level of sequencing and how to prioritise healthcare workers.
"Those examples have happened, they shouldn't have happened. They did happen. Everybody needs to learn from what happened."
Mr Reid said the important thing to do now is to really make sure the guidelines are clear and that there be a stand-by list of the right workforce.
"Plan in advance, have a back up in case some of your prioritised workforce doesn't show up on the day or you have extra vials.
"So it is really set out very clear for them - the system, don't waste vials, do prioritise those people who should be prioritised, do have a stand by list."
However, the chair of the National Immunisation Advisory Committee (NIAC) Professor Karina Butler told Claire Byrne the vaccination centres setting up did have lists and backup lists in case people didn't turn up.
“We knew that we didn't want to waste any vaccine, the centre didn't want to waste any vaccine - if someone for any reason that was scheduled, suddenly wasn't going to be able to get it, maybe became ill, for any reason - there would be people on call.
"Already people were aware we didn't want anything to be wasted.” The recommendations were to try to go through the prioritisation list, she explained.
“If there weren't people available I know that they reached out to the community for some GPs and NIAC's recommendation would always be to go through the prioritisation list to try and find people who would be suitable to get the dose.”
Prof Butler said part of the issue with the extra doses of the vaccine at hospitals last weekend was because careful administration had meant that a seventh dose had been possible from each vial.
“I want to explain what happened, it was over a weekend - in one of the hospitals in question they suddenly realised that not only had they gotten six doses out of a vial but because of their skill, because of the needle type syringes they were using, there was actually enough for a seventh dose,” she said.
“The question was, could they use that seventh dose or would they just leave it because the recommendations were just to give six doses - that prompted some discussions and it was late in the evening - this vaccine has a very short life once it's drawn.
“It wasn't an authorised dose and so you felt that anyone getting that dose had to understand the context in which it was drawn up and if they were willing to take it on that basis, then that was fine.”
Prof Butler said she understood that stories such as the ones from Dublin and Kerry are distressing for people.
“I know when stories like that come out it is very distressing, particularly for people who are waiting in the wings and perceive that it is some way delaying the vaccine that they are due.
"I can't explain every episode and every explanation I give might not account for maybe slippages that have been seen in some ways.
Sinn Féin president Mary Lou McDonald said the controversies have raised question marks.
“Nobody would be happy to hear that any vaccine is wasted, that’s the last thing we want to see,” Ms McDonald told RTÉ’s Today With Claire Byrne show.
“But the idea that there are spare vaccines that could be dispensed in accordance with just the judgment of an individual, and that in some cases those vaccines would go to family members, it isn’t acceptable.
“In fairness, the master of the Coombe has acknowledged and has apologised. This can’t happen again.
“The wider concern is the necessity for very, very clear guidance in a timely fashion so that all those who are charged with dispensing these vaccines, safely and in an order of priority, are very clear what the instruction is.
“It raises just a question mark as to why that wasn’t clear and why that wasn’t there from the get go.
“We’re not dealing with the vast, vast quantities as of yet of vaccines.
“We’re dealing with a very limited supply, so it is astonishing, therefore, that the clearest of guidance wasn’t available to everybody, given that this is such a scarce and such a precious resource at this point.”
Despite the controversy this week, Mr Reid said the vaccine rollout has gone primarily to plan.
"The pace at which the programme is rolling out is very significant, we are meeting every level of supply that we get in."
About 1.9% of Ireland’s population has been given the Covid-19 vaccine.
According to the Health Minister, by Sunday night, 94,000 vaccines were administered, with 71,000 frontline healthcare workers and 23,000 of residents and staff of long-term care facilities inoculated.