Indonesia says Australia's decision to stop processing asylum seekers from Afghanistan and Sri Lanka will be "positive" for the region's fight against trafficking.

Foreign ministry spokesman Teuku Faizasyah said the tough new policy, which has been condemned by rights watchdogs and refugee supporters, would have a direct impact on the movement of undocumented migrants around Southeast Asia.

"It will have a positive impact on the region, not just one particular country... it could be Indonesia, Malaysia or Thailand," he told AFP, referring to other countries with entrenched people trafficking syndicates.

"This is definitely a clear message to those who try to smuggle migrants, that they are only offering false hopes because there's nothing visible on the horizon," he said.

"For the network of smugglers, they will now have to think twice about sending migrants to Australia."

Critics have called Australia's move last week a knee-jerk reaction to political pressure over border security ahead of elections, but Faizasyah said Canberra gave it a lot of thought.

"What Australia has done is a process of evaluation and discussion. They must have gone through discussions and a period of thinking this through," he said, adding that the full impact would not be felt for "weeks or months".

He refused to speculate on how the hundreds of Afghan and Sri Lankan migrants in Indonesian detention centres would react to the news that they had no chance of being accepted as refugees in Australia.

In the most high-profile case, about 200 ethnic Tamil Sri Lankans who were intercepted on their way to Australia in a boat in October are refusing to leave a Javanese port until they are allowed to resettle in Australia.