Primate of All Ireland and Archbishop of Armagh Eamon Martin described the Government's stance on First Holy Communions and confirmations as a "complete reversal" of an earlier decision made on the issue.
Dr Martin also criticised the way that the communication of this new position was handled by the Government and said that it was "very disrespectful how this was done".
While such ceremonies are not prohibited under the guidelines, the official advice is that they "should not take place at this time".
The advice says: "It is advised that religious ceremonies such as Baptisms, First Holy Communions and Confirmations should not take place at this time. Further advice will follow on resumption of these ceremonies when it is safe to do so."
Speaking on RTÉ's News at One, Archbishop Martin said: "There is indeed a lot of confusion here and a lot of frustration and deep disappointment and indeed anger.
"We've been deluged with calls from parishes and I know that priests and others have been extremely disappointed by this reversal of the position that was written to us from the Taoiseach's office from the very beginning of June that said that in line with the gradual reopening of society from 5 July these ceremonies could take place.
"And so, there's been a huge amount of preparation with the children in their schools with their families."
The archbishop insisted that the Catholic Church "had been planning to do them extremely carefully with small numbers, keeping alert to all of the public health advice on gatherings after".
He said that the authorities had warned that the issue had never been with the ceremonies themselves, but that there was concern about the social gatherings that happen afterwards.
Dr Martin insisted that communions could have gone ahead safely.
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He said: "The Department of An Taoiseach wrote to us at the beginning of June basically giving us the go ahead to begin to plan and stressing to us that we should encourage families to ensure that they are going to adhere to the prevailing public health advice.
"Now put that against what happened the other night.
"A journalist's tweet and the Tánaiste dismissively saying 'oh they're off' - that was how we were told about the change in direction.
"The manner of communication in this case was grossly disrespectful and we are extremely disappointed."
"I've the letter here sitting in front of me, which was basically giving us the go ahead to begin to prepare to celebrate these sacraments from 5 July."
A statement issued on behalf of Leo Varadkar this afternoon said: "The Tánaiste is very aware of the importance of these occasions. He gave an on-the-record reply to a question at a press conference. It wasn't an off the cuff remark as has been suggested.
"Unfortunately, the public health advice from our doctors and scientists is that people who are unvaccinated should avoid mixing indoors. It may well be the case that the Government could have communicated this more effectively."
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Families of children due to receive church sacraments have expressed frustration and upset at the way they were informed that the ceremonies, many of which have postponed several times, will not go ahead.
Lucy Dowling, from Glasnevin in Dublin, was expecting to wear her third communion dress next Wednesday.
Since Tánaiste Leo Varadkar's "they're off" comment earlier this week, Lucy's mother Wendy had been trying to find official confirmation.
"We scoured the internet looking for some kind of wording and there was nothing," she said.
"Then this morning we got an official email from the priest in the parish, to say it was off."
Confusion over whether the National Public Health Emergency Team had recommended the postponement was also a frustration for families.
Matthew O'Connor, from Donabate in Dublin, was due to make his confirmation later this month.
His graduation from primary school was celebrated on Zoom, so his family was looking forward to this "rite of passage".
"We understand the need for public health measures but when you hear that it's not public health advice and the Government decides to make a policy on the fly during press conference, that's very worrying," said his mother, Lucy O'Connor.
At this evening's NPHET briefing Deputy Chief Medical Officer Dr Ronan Glynn said while it "wasn't a direct piece of NPHET guidance produced on Monday" to cancel religious ceremonies, such as baptisms, communions and confirmations, it "reflects the views of public colleagues across the country."
Additional reporting Sharon Tobin
