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.
Mr 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 Government's 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.