Deputy Prime Minister Barnaby Joyce has called for unity in wake of explosive tensions between Prime Minister Malcolm Turnbull and Tony Abbott.

The comments come after Mr Turnbull announced the Defence Department and the Australian Federal Police will investigate the leak of sensitive national security documents published in newspapers on Wednesday along with quotes from Mr Abbott.

The article by The Australian's Foreign Editor Greg Sheridan reported that a draft defence white paper produced under Mr Abbott would have seen the 12 submarines to be commissioned by the government built early.

Deputy Prime Minister Barnaby Joyce, Prime Minister Malcolm Turnbull and Minister for Foreign Affairs Julie Bishop during Question Time at Parliament House in Canberra on Monday 22 February 2016. Photo: Alex Ellinghausen Alex Ellinghausen

"I'm not just disappointed, I'm flabbergasted at this decision," Mr Abbott told the newspaper. He subsequently denied he leaked the excerpts of the paper.

Mr Joyce said on Thursday that the Turnbull government's honeymoon was over and it was time to stick together.