About 1,500 chicks were discovered close to an avian flu exclusion zone on the outskirts of Crowland on Friday.
The RSPCA said it was not possible to rehome them due to the possibility of infection.
The charity said it was possible that prior to being dumped, the chicks were being offered for sale.
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The RSPCA said the chicks' farmer had been found and it was likely the birds had been passed to a third party by a "rogue member of staff" and then offered for sale from the back of a van.
They said the farmer was co-operating with the RSPCA investigation.
Insp Justin Stubbs, of the RSPCA, said the chicks were found close to an avian flu exclusion zone, which meant they could not be sold on.
"Sadly, the owner has had no choice but to euthanise them," he said.
Some were found dead, or dying, suffering from exposure and being picked off by predators, Mr Stubbs said.
Describing the case, Mr Stubbs said: "I would consider this to be one of the most callous acts I have come across in 20 years with the RSPCA."
The charity said it wanted to hear from anyone in the area who was offered any of the chicks.
Hundreds of newborn chicks found abandoned in a field in Lincolnshire have had to be put down, the RSPCA said, due to a case of bird flu nearby.