The Turnbull government could improve the budget bottom line by $350 million by scrapping taxpayer support for religious organisations.

The Parliamentary Budget Office has found the government could raise an extra $390 million over the forward estimates by scrapping tax concessions for religious organisations, although about $100 million would go to the states as GST.

It could also save $60 million by ending support for the controversial National School Chaplaincy Program.

The research was done for libertarian crossbench senator David Leyonhjelm, who says the government should consider the move.