This could lead to warning labels on medical marijuana within a year.
Scientists analyzed 27 studies of the links between marijuana and cancer in humans.
Not all the studies showed a link, but regulators say they found that marijuana smoke was clearly shown to cause cancer.
Voters in 1996 approved a measure that made medical marijuana legal in California.
Supporters included patients with serious illnesses such as cancer and AIDS.
They said pot helped them manage pain and nausea.
Some medical marijuana advocates took issue with the state's warning.
They countered that researchers have long known that the smoke contains cancer-causing compounds.
However, Kris Hermes, spokesman for the pro-medical marijuana group Americans for Safe Access, told news reporters, "This does not mean in any way that those carcinogens that appear in smoked marijuana, smoked cannabis, have any kind of causal relationship to cancer."
The Associated Press contributed to this report.