Mr Morrison and Nationals leader Michael McCormack were forced to reshuffle the ministry following a leadership spill in the Nationals party.
Mr Littleproud, the newly-elected deputy, had held the water, drought and emergency management portfolios since last year’s election, and held agriculture before that.
He took up the agriculture portfolio in 2017, when he was first promoted to Cabinet.
Victorian Darren Chester will return to Cabinet with his veterans affairs portfolio, and Queensland backbencher Keith Pitt will move into Cabinet with the mining, resources and Northern Australia portfolios.
The resources and agriculture portfolios were until now without ministers after scandal and political infighting forced two resignations in the junior coalition partner in as many days.
Bridget McKenzie quit cabinet over the sports rorts affair, while Matt Canavan went to the back bench after supporting Barnaby Joyce’s failed leadership tilt.
While Senator McKenzie was forced to resign over undeclared gun club memberships, she retained the senate leadership of the party. Senator Canavan has remained deputy leader in the upper house.
— with AAP