Marty Natalegawa was commenting after a boat carrying 34 people from four countries was found drifting ashore in West Java on Wednesday.
"Can such an (Australian Prime Minister Tony) Abbott administration policy be called the policy of a government that upholds human rights and humanity?" he was quoted saying by Kompas newspaper.
"Those asylum seekers are people that need protection."
The Australian broadcaster ABC aired footage last week of a boat carrying refugees being towed by an Australian vessel. The boat in the video is believed to be the one that washed ashore in Indonesia.
Natalegawa urged international human rights groups and the UN to scrutinise Canberra's new policy of intercepting illegal immigrants at sea, noting that Australia is a party to the 1951 UN refugee convention.
However, he said it was not the Indonesian government's policy or intention to help the illegal boat traffic.
Both countries, he added, were affected by refugees, many of them South Asians who reach Indonesia before attempting to get to Australia.