Sydney Morning Herald journalist Paul McGeough says footage captured of the recent deadly raid on a Gaza aid flotilla has been re-edited for Israeli purposes.

Mr McGeough was onboard the flotilla with another Fairfax journalist when it was raided earlier this month, killing nine pro-Palestinian activists.

He has told triple j's Hack program his equipment and footage were seized by Israeli officials before he was deported.

"The imagery that was in various cameras is now being edited and put out by the Israeli Defence Force as their account of the events on the ships," he said.

Mr McGeough says Fairfax and Australian authorities are working to have the property returned.