The RSPB said High Pathogenic Avian Influenza (HPAI) is affecting a range of poultry operations across the UK.
Wild bird species involved are mostly geese, ducks and swans, but a number of birds of prey have also been confirmed to have died.
People in the West Midlands were urged not to touch or feed any sick or dead wild birds after the cases were reported last month.
Around half a million birds have been culled so far, according to UK chief veterinary officer Christine Middlemiss, who said there are 40 infected premises in the UK – 38 in Great Britain including 33 in England.
An Avian Influenza Prevention Zone was declared across the UK on November 3 before being extended on November 29 with the added requirement all captive birds have to be kept indoors, amid concerns that wild birds migrating from mainland Europe during the winter are carrying the disease.
The risk to human health from avian influenza remains very low, according to public health advice, and there is a low food safety risk.
Speaking in the House of Commons, Environment Secretary George Eustice said: “Each year the UK faces a seasonal risk in incursion of avian influenza associated with migratory wild birds.
“While we have that each year, I have to say this year we are now seeing the largest-ever outbreak in the UK of avian influenza with 36 confirmed cases.”
Defra confirmed the most up to date figure is 40 – 33 in England, three in Wales, two in Scotland and two in Northern Ireland.
Dr Middlemiss told the BBC the “phenomenal level” of bird flu has “huge human, animal and trade implications”.
She said the disease is being spread by migratory birds flying back from the north of Russia and eastern Europe.
The vet warned the UK is only a few weeks into a migratory season that goes on until March.
“We are going to need to keep up these levels of heightened biosecurity for all that time,” she said.
The protection zone means that in addition to keeping birds and poultry housed, keepers must continue to take precautions such as regularly cleaning and disinfecting clothing, equipment and vehicles and limiting access to non-essential workers and visitors.
Defra has said the new housing measures will be kept under regular review.
Dr Middlemiss said she is “very concerned” about bird flu, and that having 40 infected premises is “a really high number for the time of year”.
She told BBC Radio 4’s Today programme that around half a million birds have had to be culled.
“I know that sounds a huge number, and of course for those keepers affected it’s really devastating.
“But in terms of food supply impact it’s actually relatively a very small number in terms of egg supply, meat, chicken and so on.”
She said they are continuing to get new detections, adding she confirmed another two on Wednesday night.
Dr Middlemiss said people who keep chickens and want to feed wild birds need to make sure everything is kept “scrupulously clean” and “absolutely separate” to avoid infecting their own flocks.
She said there is an ongoing background risk of bird flu every year, adding that previously there would have been a reasonably sized outbreak followed by two or three quiet years.
“But that’s not happening,” she told the Today programme, adding this is being seen across Europe, with outbreaks last year and some over the summer.
“And now we’ve got this massive increase with the migratory wild birds, and absolutely it’s something we need to understand better about why we are getting these ongoing infections every year,” Dr Middlemiss said.
Paul Walton, head of habitats and species at RSPB Scotland, said: “The presence of the High Pathogenic Avian Influenza virus in all UK countries, in both poultry premises and wild birds, and the high numbers of dead and sick birds now seen, is generating growing concern among conservationists and nature lovers.”
Another RSPB spokesperson said: “Everyone should take care to maintain good hygiene when feeding garden birds, regularly cleaning feeders outside with mild disinfectant, removing old bird food, spacing out feeders as much as possible, and washing your hands.”
The bird flu outbreak is not expected to have any impact on the supplies of turkeys or other birds over Christmas.