Bangkok: Photographs splashed in the Philippine media of Australia's top overseas spy Nick Warner meeting with President Rodrigo Duterte have raised concerns about Canberra's engagement with the region.

Australian Defence Minister Marise Payne later defended Australia's efforts to step-up engagement with south-east Asia where political and other freedoms have stalled under increasingly authoritarian governments.

The United Nations has accused Mr Duterte, a boastful, foul-mouthed former provincial mayor, of presiding over a so-called war on drugs that could amount to crimes against humanity.

The meeting between Mr Warner and Mr Durerte at the presidential palace in Manila came a day after Foreign Minister Julie Bishop had said Australia was "deeply concerned" about an escalation of the crackdown which has left more than 12,000 Filipinos dead.