Thousands of hens have had to be slaughtered because their cages did not meet modern EU standards.
The Department of Agriculture said it had to ensure that European regulations were complied with - and the birds had to be killed ahead of their normal life cycle.
Over ten years ago, the EU directed that battery cages should be replaced by enriched cages - giving hens more space for roosting, nesting and scratching.
A ban on the sale of eggs from cages that had not been modernised has been in place since 1 January.
Most egg producers have updated their facilities. But in November, the EU was informed that ten farmers were not ready to fully comply with the new rules.
Following inspections in recent weeks by the Department of Agriculture, nine of the flock-owners had to cut back their hen numbers, which meant the hens were sold into the food chain ahead of the normal cycle.
It is estimated that about 100,000 hens had to be killed early because of the new regulations.
Owen Brooks of the Irish Egg Association said all the actions were taken in agreement with the farmers concerned, and that the number of birds involved was small in the context of the size of the national flock.
The Department has repeated that eggs from old cages will not be allowed onto the market.
Up to a few years ago, there were over 90 farmers with 1.2 million birds in cages. But because of the new regulations the number of producers has dropped by two-thirds to about 30.
Many farmers got out of the business because they needed extra space to be compliant.
Those who remained in business scaled up and there are now about 1.4 million hens in cages.