The Morrison government is facing an internal rebellion by Nationals MPs over plans for a new anti-corruption regime unless it protects ministers from being targeted over infrastructure grants made against bureaucrats' advice.

Some MPs were shocked this week when the minority government waved through a motion calling for a national integrity commission without a debate in the Coalition party room.

Former deputy prime minister Barnaby Joyce issued a warning over any national integrity scheme. Credit:AAP

Nationals MPs have now warned they will oppose the scheme unless Attorney-General Christian Porter ensures it would not allow ministers to be fingered for corruption if they ignored departmental advice and approve grants for projects in rural or regional areas.

The government is expected to announce its policy imminently to prevent a humiliating loss in Parliament, with crossbenchers confident they have the numbers to force a vote.