The H3N8 flu has been associated with the deaths of harbour seals in the US last year.
Researchers say the virus may have evolved from a type that had been circulating in birds, the 'BBC News' reported.
Scientists claim the discovery highlights the potential for pandemic flu to emerge from unexpected sources.
"We need to be very nimble in our ability to identify and understand the potential risks posed by new viruses from unexpected source" said Dr Anne Moscon.
"It's something that's been circulating for a while in birds, but we've not had this sort of die off relating to this virus in the past. As we've looked at it in some detail, we've found there have been mutations in this virus which enable it to bind to both bird receptors for flu as well as mammalian receptors for flu," said co-authors of the research, Prof Ian Lipkin, from Columbia University in the US.
Lipkin told the BBC that finding this flu virus in seals was an interesting "new jump".
As well as mutating to live in both animals and birds the scientists say this flu has evolved to make it more likely to cause severe symptoms. The virus also has the ability to target a protein found in the human respiratory tract.
"There is a concern that we have a new mammalian transmissable virus to which humans haven't yet been exposed. It's a combination we haven't seen in disease before," said Dr Anne Moscona of Weill Cornell Medical College in New York.
One of the big concerns, according to Lipklin, is that seals are acting as a mixing vessel for viruses in a way that has previously happened in pigs.
"What was interesting about this is the seals are acting as an intermerdiary - they have receptors for both bird flu viruses and well as mammalian flu viruses, so you have a host in which this virus can adapt, evolve and become more mammalian in phenotype and more capable of causing disease in mammals," said Lipklin.
"That's when we really need to be concerned that it's going to be spreading into humans."
The report is published in the journal of the American Society for Microbiology.