A number of AI centres purchased sires on the basis of the original EBI rankings, and are now understood to be concerned about the impact the adjustment may have on demand for the semen.
ICBF's Kevin Downing told the Farming Independent that the problem had been compounded for "a lot of farmers who weighed in very heavily on one, two or three genomically selected bulls, and that is where some of them are really getting hit".
He said that the problem had been caused by a "system software issue whereby a small number of bulls were given more inflated figures than they deserved, and they are the ones where over €100 is coming off" against an overall average reduction of €39.
Mr Downing said it was "understandable" that farmers would be angry, particularly those who bred a lot of cows to a sire with an EBI that had dropped significantly as a result of the error.
He said measures had now been put in place to ensure there is no repeat occurrence of the software problems.
An ICBF survey on 367,000 births from AI in 10,338 herds during 2016 found that only one bull was used for up to 80pc of the calves born on 11pc of the farms - and on 48pc of farms, up to 40pc of the calves were by one bull, a practice which is not recommended by ICBF.
Irish Holstein Friesian Association (INFA) CEO Charles Gallagher described the situation as "deeply disappointing" and said "there are implications (for our association) in ensuring the accuracy of the herd book entries."
He said that the IHFA, which has two representatives on the ICBF board, has been "looking for changes to the way that the EBI evaluations are carried out for some time and we will now be pressing that they are made".
A spokesperson for ICMSA said the priority for both ICBF and the AI companies must be an immediate clarification of the situation around the semen sold to many farmers and its subsequent downgrading.
"Farmers bought and paid for this in good faith and it is of the first importance that clarity is brought to their situation and that they know exactly and in good time what the next steps are in this process of repairing this situation."
In a letter issued over the weekend to more than 10,000 farmers who use AI for breeding, Sean Coughlan, CEO ICBF, urged farmers to use a team of at least five high EBI sires, and preferably up to seven sires spread evenly over their herds.
"A single AI bull should never be used on more than 20pc of your herd.
"Overuse of a single bull leaves your herd more vulnerable to EBI fluctuations.
"Now that all dairy AI proofs have been updated, we would encourage HerdPlus members to (re)run 'Dairy Sire Advice' for their herds," the letter added.