Bali: Justice Minister Michael Keenan has urged Australians to ensure they are donating to legitimate charities after a report revealed there was a high risk of terrorism funding being channelled through non-profit organisations.

The warning comes days after the Department of Foreign Affairs and Trade suspended the funding of World Vision programs in the Palestinian Territories after Israel claimed the head of the charity in Gaza was bankrolling Hamas.

Mohammed Al Halabi, right, is seen talking to children in his work as Gaza program manager for World Vision. Credit:World Vision International

"We do make very large donations to charities and the nature of that money is that a lot of it goes overseas," Mr Keenan said at a counter-terrorism summit in Bali.

"So clearly that is something that we need to be concerned about and we have seen an example highlighted in the Middle East as recently as this week that some of that money can be diverted to the wrong purposes."