Dr Natalegawa on Tuesday attended a Bali forum that Prime Minister Tony Abbott pulled out of at the last minute.
Canberra blames the coming budget for Mr Abbott's absence, but it's understood he didn't want to meet President Susilo Bambang Yudhoyono while Australia was engaged in its inflammatory border policy.
The Indonesian navy found 20 asylum seekers on a remote island on Sunday.
The men from India and Nepal claim Australian authorities added three people - two Albanians and an Indonesian - to their boat before sending it back to Indonesia.
Dr Natalegawa says it's a worrying report.
"If confirmed, obviously this is a very serious development," he told reporters in Bali on Tuesday.
"As I've said from the very beginning, we are risking a slippery slope."
The minister also said the latest Australian operation showed the Abbott government policy wasn't working.
"The policy of his government to push, unilaterally forcing asylum seekers - which is threatening and violating their human rights - it's not yielding (success) because such efforts are still being conducted," Dr Natalegawa said.
The asylum seekers were found stranded on Lay Island in East Nusa Tenggara, and are aged from 17 to 43, most of them in their 20s.
Meanwhile, the Indonesian government still has not been given an explanation for Mr Abbott's decision not to meet SBY in Bali.
It was seen as a chance to push along the reconciliation process after last year's spy scandal.
Dr Natalegawa said he didn't wish to speculate on whether the budget or the asylum-seeker operation was the cause.
"I'm certainly not a mind reader and I haven't been able to ascertain exactly what it is that is making it impossible for the prime minister to be in Bali at this time," he said.
He also didn't want to make it something "bigger than it is".
"That's something that only the Australian government could answer," he said.
"What matters most is that we invited them.
"That they didn't come, that's their choice."
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