The Californication actor is to replace Andy Garcia as the head of a Soviet special forces team who are on secret mission, according to Variety.
Phantom centres on a Russian captain who has to deal with a maverick KGB unit and a ghost while undersea.
He will be joining confirmed stars Natasha McElhone, William Fichtner and Ed Harris, under the direction of Lonely Hearts director Todd Robinson.
Robinson, who wrote Ridley Scott's water thriller White Squall, will be directing from his own script.
Duchovny has just wrapped Goats with Ty Burrell and Vera Farmiga.
The film sees him playing a character called Goat Man, who enters into the life of 15-year old Ellis, who has been sent to a boarding school on the East Coast.
He has also joined the cast of Relative Insanity, a contemporary New York-set update of Chekhov's classic play The Seagull.
The star can currently be seen starring in the fifth season of Californication, where he plays the writer Hank Moody, a man contending with his difficult relations with his ex-wife and daughter.