Canine influenza has been confirmed in two dogs in Essex County.
The cases of H3N2 virus is believed to be the first instance of the disease in Canada.
The dogs in question had been imported from South Korea through the United States.
The day after they arrived the dogs showed signs of respiratory disease.
A veterinarian has examined the dogs.
Acting Medical Officer of Health Dr. Wajid Ahmed says the puppies are isolated right now.
"They are self quarantining within their homes," he says. "We are following up with the families to make sure they are following all the public health guidance as they should."
He says there is little chance this flu strain can be spread from dog to human.
"It is very unlikely for these canine influenza to spread to humans. It typically tends to just transfer from one dog to another."
The concern is that the disease is easily transmitted between dogs and several other dogs are showing signs of respiratory disease.