The film is being directed by Julius Onah and also star Noomi Rapace, said the Hollywood Reporter.
An adaptation of the Marcus Sakey novel, the film has been scripted by David Koepp.
Smith left the project citing scheduling conflict.
Sakey's book takes place in a world where a rare set of people are born with extraordinary abilities and are called "brilliants".
If Leto decides to take on the role, he'll play a federal agent with great hunting gifts who is drafted to hunt down a terrorist, another such brilliant who intends to start a civil war.