Bransby Home of Rest for Horses has been shut to the public after an outbreak of equine flu.
The virus was identified on Tuesday (11 May) and the source of infection is not yet know.
Bransby has 271 horses and the charity estimates about 80% of the animals are infected.
The Lincolnshire based-charity has been forced to cancel its open day on Sunday 6 June, but is hoping to be reopen to the public in time for the school summer holidays.
Equine welfare manager Sally Howard said she was “devastated”.
“This will have serious consequences for the charity and the horses it cares for, especially over the next couple of months,” she said.
“Staff are always extremely careful to ensure all animals that are received by the charity are put into quarantine for at least four weeks and are then thoroughly tested before being allowed to mix with the herd.
“Some horses are likely to become very poorly and there is the possibility that older and weaker ones may need to be euthanased, which is, of course, a matter of last resort and great regret.
“We will do all we can to contain the disease and to relieve the suffering of those affected. And we would urge other owners to get their horses vaccinated.”
Bransby is entirely funded by public donations and none of the horses were vaccinated against the virus due to the high cost of protecting 271 animals.
This is not the first time the centre has been affected by an infectious disease.
From 2006 to 2008 Bransby was shut due to an outbreak of the highly contagious respiratory disease strangles. It reopened in November 2008.
Ms Howard added: “We had just got back on our feet and had visitors coming in and now we’ve had to close the doors again. This is a shorter closure than with strangles but will affect us financially.”