The minister's car was attacked by unidentified militants outside the gate of the transport ministry here, Xinhua reported citing a source in the minister's office.
The source added that the gunmen fled the scene after the shooting and security forces are trying to hunt them down.
The assassination attempt is the third of its kind since Bathib took office in 2011.
He is a member of the current unity government formed last year under the Gulf-brokered power transfer deal that gave an equal number of seats to the ruling General People's Congress and opposition parties.
Yemen's security situation is deteriorating as crime rates are on the rise and terrorist groups are active across many parts of the country.