However, a spokesman for the Department for Environment, Food and Rural Affairs said it was not notified and did not order the cull.
An RSPCA spokesman said: “Very sadly, the RSPCA has learned that the surviving chicks which were dumped in a field in Crowland on Friday have been put to sleep due to a case of avian flu nearby. We are sorry to hear of this outcome.”
The RSPCA was called after people spotted the chicks running around. Members of the public helped round them up and put them in boxes for warmth.
A third party is believed to have taken the chicks from a nearby breeder and then dumped them. The breeder was alerted and took the chicks back.
Some had died and some had to be put down due to injuries but many were thought to be in good health.
An RSPCA statement said the breeder is fully cooperating and assisting with investigations.
RSPCA inspector Justin Stubbs said: “For someone to dump these vulnerable chicks is unbelievable.”
Anyone with any information who was responsible should contact the RSPCA on 0300 123 8018.