The disease has been identified in two ferrets and a cat, and it appears the animals caught it from their sick owners.
The cat, 13, was in Iowa and the two ferrets with the disease were in Nebraska and Oregon.
The virus, which has infected millions of people, had previously been detected only in pigs.
The World Organisation for Animal Health said the cases were no cause for concern, and there was no evidence that animals played any role in the spread of the novel influenza virus.
Colorado State University's Veterinary Diagnostic Laboratory confimred it would begin testing samples from pets submitted by veterinarians for H1N1.
Kristy Pabilonia, a veterinarian and expert on H1N1 testing in animals at the university, said there was no evidence of pets passing H1N1 to people.
"At this time, there are very few cases of H1N1 in pets so we don't think that people need to be overly concerned," she said.
However, if someone in a household with a pet becomes ill with H1N1, they should watch their pet for symptoms and know that there is a chance that the animal could get sick.
Pabilonia said because this strain of H1N1 is new, information about how it impacts animals is limited. It is possible that any animal may be susceptible to H1N1, but no other cases have been documented in companion animals.
People with the flu should be careful when in contact with their pets, practicing social distancing with pets as well as people. People who are ill should wash their hands before handling pets and, if possible, someone who is well should feed and care for pets.
Just like people, pets are exposed to H1N1 through aerosols - fluids released when someone sneezes, coughs or touches their face and then a surface.
Because there have only been a few cases of H1N1 flu in pets, veterinarians have limited information about the symptoms. Pets with H1N1 may behave as if they aren't feeling well, acting lethargic and may appear to have a respiratory illness. If a pet seems ill, it should be taken to a veterinarian as soon as possible and the veterinarian should be alerted that the pet has been exposed to someone with influenza.
The World Organisation for Animal Health said it was closely monitoring the situation.
"Pandemic H1N1 2009 virus infections in pigs and other susceptible animals were assessed as probable from the very first days after the virus was detected in humans," said its director-general, Dr Bernard Vallat.
"So, it does not come as a surprise that notifications of infection in new animals species are received; on the contrary it demonstrates animal disease surveillance is efficient and functioning to the benefit of all.
"So far, no evidence has suggested that animals play any particular role in the epidemiology or the spread of the pandemic H1N1 2009 virus among humans.
"Instead, investigations led by competent national authorities point to possible human-to-animal transmission in most cases.
"For this reason, the OIE considers that it is sufficient to certify the healthy state of animals for international trade during the relevant period before their exportation and maintains its position that no specific measures, including laboratory tests, are required for international trade in live pigs and other susceptible animal species and/or their products.
Vallat said laboratories with expertise in animal influenza across the world have been sharing biological material and information, and have been working to assess transmission mechanisms in different species of animals.
"The experiments demonstrated, among other things, at an early stage that pigs are susceptible to the pandemic H1N1 2009 virus but that infected pigs only showed mild signs of disease.
"As national veterinary authorities continue and intensify surveillance for the pandemic H1N1 2009 virus in susceptible animals, it is very likely that there will be additional findings of other influenza strains," Vallat said.
"That is why we insist on the importance of epidemiological investigations of unusual illness among all animals, and the necessary collaboration and communication between animal health and public health authorities."
The Ontario Veterinary College and the Animal Health Laboratory at the University of Guelph said ferrets are susceptible to various influenza viruses.
"Although the risk of human to pet transmission of pandemic H1N1 is presumably very low, proper measures should be taken by people who have influenza to reduce the risk of transmission to other household members and to pets, such as paying close attention to hygiene, especially after touching animals, and avoiding close contact with pets' faces.
"If your pet is coughing and sneezing or showing other signs of illness - such as lethargy or lack of appetite - consult a veterinarian. Follow common sense infection control measures: Wash your hands regularly and thoroughly, especially after handling animals. It is a good general idea to make sure your physician knows whether you own pets or have other animal contact."
Influenza is, first and foremost, a disease of birds. However, strains affect people, horses, pigs, cats, dogs and ferrets.