Grassroots Nationals members had to foot the bill to pay Barnaby Joyce a salary for six weeks after the Deputy Prime Minister was thrown out of Parliament and lost his $416,000-a-year job.

Fairfax Media can reveal the previously undisclosed arrangement involved the use of party funds to give the Nationals leader a wage while he was campaigning to win the December 2 byelection triggered by the dual citizenship crisis.

The arrangement came to light after another difficult day in Parliament in which the Deputy Prime Minister's use of an Armidale apartment for six months rent-free formed the basis of a Labor attack on Mr Joyce's authority and credibility.

Prime Minister Malcolm Turnbull and Deputy Prime Minister celebrate on the night of the December 2 byelection. Credit:Alex Ellinghausen

Mr Joyce's office confirmed late on Wednesday the Nationals leader was paid a salary during the campaign, but said it had been advised by the party that it is "not unprecedented for candidates to receive a form of income in exceptional circumstances".