The H5N1 testing facilities are on the flagship USS Blue Ridge and the carrier USS Kitty Hawk, said Rosemary Tan, chief executive of Veredus Laboratories.
Veredus, founded three years ago, also makes malaria and dengue test kits and was approached by the US Navy over a year ago.
The Japan-based Seventh Fleet has 50 vessels and 20,000 active personnel who conduct missions in such bird-flu hot spots as Indonesia, Malaysia and other Asian countries.
On-board testing capabilities had become "essential", The Straits Times quoted fleet surgeon Captain Charles Baxter as saying from Yokosuka, Japan.
He told the newspaper that the DNA-based test kit was one of the most advanced in the market.
It requires only a small blood sample from the test subject. Results are available in four hours, compared with 10 days for other kits.