"I am advised that all people have been accounted for," he said.
Agus Barnas, a senior official at the co-ordinating ministry for political, justice and security affairs, reiterated Suyanto's tough stance, telling AFP that Indonesia "rejects taking asylum seekers, that's our stance for the time being.
"We are still negotiating with Australia on this matter."
In Australia, Abbott faced questions about whether the stand-off signalled his hardline policies were a failure, but would only respond by saying that Canberra has "good and improving cooperation with Indonesia".
"Everyone in the official establishment of Indonesia understands that it is in Indonesia's national interest, just as much as it is in Australia's national interest, that the scourge of people smuggling be eliminated," he said.
Some critics have accused Australia of abandoning its obligations to the UN convention on refugees through its new policy.
Tensions between Jakarta and Canberra rocketed in the past week after the Sydney Morning Herald newspaper reported that Australian missions across Asia, including the one in Jakarta, were involved in a US-led spying network.
The paper amplified a report in German weekly magazine Der Spiegel, which was based on leaked documents from fugitive intelligence analyst Edward Snowden.
The allegations of espionage prompted Indonesia to summon the Australian ambassador, while Foreign Minister Marty Natalegawa declared "enough is enough".
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