Some cages for hens provide a "necessary defence" against bird flu, the government's chief vet has said.
In a tweet, Nigel Gibbens said the larger pens, which replaced so-called battery cages in 2012, have welfare benefits and offer more space.
It comes after 10 leading British vets, who believe caging hens is unethical, said his "brazen endorsement" was "extremely disappointing".
They said the restricted space was "seriously detrimental to welfare".
Battery cages for chickens were banned in the EU in 2012. The ruling said that if laying hens were to be held they must be in enriched – also known as colony – cages instead.
The enriched cages provided extra space to nest, scratch and roost and the guidance from the Department for Environment, Food and Rural Affairs (Defra), is that each bird in an enriched cage must have at least 750 square centimetres of space.
The minimum for battery cages was 550 square centimetres.
Despite the banning of battery cages, a number of leading retailers have announced that they are moving towards selling free-range eggs only.
But at the Egg and Poultry Industry Conference in October, Mr Gibbens called this a "regrettable move" and said cages "have a lot going for them".
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Criticising him in a group letter to the Times, 10 vets said overcrowding and restricted space were "seriously detrimental to welfare".
"Hens in cages cannot carry out fundamental species-specific behaviours", they added.
The group dismissed his claims about protection against bird flu saying there are other options to manage the threat and urged the chief vet to take a "more progressive position".
Mr Gibbens later defended his view on Twitter and said: "Free range risks disease that is really bad for welfare."
Skip Twitter post by @ChiefVetUK
Colony cages offer welfare benefits and more space than the battery cages that they replaced. Housing is a necessary defence against avian flu at times of high risk. Obliging free range risks disease that is really bad for welfare. https://t.co/9H2tvUsnO8
— NigelGibbensChiefVet (@ChiefVetUK) December 2, 2017
End of Twitter post by @ChiefVetUK
A Defra spokeswoman said: "Enriched cages offer less exposure to the threat of bird flu during an outbreak than free range systems, and provide more floor space and more height than battery cages."
