Australia's new agriculture minister has distanced herself from the National Party leader's policy to pray for rain.

Deputy Nationals leader, Victorian Senator Bridget McKenzie will become the first woman to serve as Agriculture Minister when she is sworn in with the new Cabinet on Wednesday.

"I am a person of faith, so I do pray for rain but I also believe in the separation of church and state," Senator McKenzie said.

"So whilst I personally pray for rain, I think as Minister for Agriculture, working closely with David Littleproud as minister responsible for the drought taskforce, I believe in getting practical responses on the ground to those farmers doing it tough at the moment."

It comes after Nationals leader Michael McCormack said praying for rain was one of his drought response policies.

"One of many policies, I will always pray for rain, I pray for lots of things. I think people should pray more, it's a good thing to pray," Mr McCormack said.

"The fact is, we've got to do more than pray. We've got to put in the right policies, we've got to be practical and pragmatic about it and that's what we're doing … we're keeping a watchful eye on it."

Littleproud gets new role

Prime Minister Scott Morrison's decision to give Senator McKenzie the agriculture portfolio comes at the expense of Queensland Nationals MP David Littleproud, who has held the job for 16 months.

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"The deputy leader of the National Party wanted agriculture and when you're the deputy leader you get to pick, that is only fair, and I know Bridget will do a good job," Mr Littleproud said.

Mr Littleproud remains in Cabinet as Minister for Water Resources, Drought, Rural Finance, Natural Disaster and Emergency Management.

Queensland Senator and Minister for Resources and Northern Australia, Matt Canavan also remains at the cabinet table, but the Nationals hopes of retaining a fifth spot in cabinet following the retirement of NT Senator Nigel Scullion, were dashed in the new ministry.

Barnaby Joyce wants water and agriculture as one ministry

Senator McKenzie is the seventh agriculture minister to be appointed in 12 years and will be joined in the 46th Parliament by former agriculture ministers Littleproud, Barnaby Joyce, Joel Fitzgibbon and Tony Burke.

Mr Joyce, who also served as water minister, argued the portfolios should be represented by the same minister.

"Agriculture and water should have been kept together … separating them has the capacity to turn it back into purely an environmental portfolio rather than looking after the socio and economic issues of the inland regional towns that rely on irrigation," Mr Joyce said.

NFF welcomes McKenzie appointment

The National Farmers Federation welcomed Ms McKenzie's appointment and paid tribute to Mr Littleproud.

"Senator McKenzie has been a long-time vocal and effective advocate for regional and rural Australia," NFF president Fiona Simson said.

"Under minister Littleproud's leadership, bipartisan support for the Murray-Darling Basin Plan prevailed, $1 per litre milk came to an end, and significant improvements were made to the regulations governing the export of live sheep to the Middle East."

Senator McKenzie's appointment is one of several going to regional women, including South Australian Senator Anne Ruston, who becomes Minister for Families and Social Services, and NSW MP Sussan Ley who will serve as Environment Minister.

Western Australian MP Nola Marino is Assistant Minister for Regional Development and Territories and Tasmanian Senator Johnathon Duniam is the Assistant Minister for Forestry and Fisheries.