Animal Health Australia, the not-for-profit body overseeing the guidelines, says it's the biggest response to a public consultation so far.

It's the first time in 15 years the community is having a say on the national poultry guidelines but animal welfare experts are concerned the industry's power means caged eggs won't be phased out.

Experts claim battery cages prevent hens from performing natural behaviours and leave them with weak bones, fractures, and osteoporosis.

But Egg Farmers of Australia argue battery cages are not the inhumane system social media and bad press have impressed on the public.

Chief Executive John Dunn told AAP that cages, despite their reputation, meant less disease, lower mortality, less infighting or cannibalism, no use of antibiotics, better biosecurity control and food safety.

"Because there is less disease, fewer birds die," he said on Wednesday.

If approved the draft guidelines would replace the current voluntary system for poultry standards with the aim of improving animal welfare.

Animal welfare experts say the guidelines will be a test for the federal government.

"The government's objective of promoting a productive agricultural industry is in conflict with animal welfare standards," RSPCA senior policy member Dr Jed Goodfellow told AAP.

"Animal welfare costs cut into agricultural profit."

The draft guidelines call on community and scientific comment but Dr Goodfellow said many researchers won't speak out for fear of losing funding.

He's called for an independent animal welfare commission to improve the transparency around animal welfare across all industries in Australia.

University of Queensland animal welfare Professor Clive Phillips backs an independent commission, saying any animal welfare research is "very carefully" managed by the industry to "get the answers they want".

He said the government needed to look at what the public wanted - with many consumers now switching to free range eggs instead of caged.

Prof Phillips said the government was not looking to the future of egg producers to sustain them in a system the public accepted.

But Mr Dunn said egg farmers had gone to great lengths to open farms and show people battery conditions were not what they think.

"We're exhausted, we're pretty tired from the work we've done to open our farms and get community members in," he said.

A spokeswoman for federal Agriculture Minister David Littleproud told AAP the responsibility of animal welfare fell on state and territory governments.

Submissions on the draft guidelines close on Monday.

Australian Associated Press