ISO 14001 is a management standard that helps organisations minimise how their business negatively affects the environment.
Honda, which last year launched its environmental concept and still races with an image of the globe on its livery, is the first F1 team to implement the standard.
The statement said Honda, whose factory was inspected by SGS Group, will now work on "specific targets to reduce its CO2 emissions".
The team "has shown clearly how certification to ISO 14001 can form an important part of its business and marketing strategy," said inspection group SGS managing director Pauline Earl.