"We just found this out now, well, just yesterday," he said.
As there had been no tip, the men had not been monitored, he said.
"While we've always known the risk of pilots with extreme views, we didn't imagine something like this," he said.
Australia and Indonesia signed a code of conduct on intelligence in August last year to mend damage from 2013 leaks revealing Australian spies targeted the phones of then President Susilo Bambang Yudhoyono, his wife and confidants.
It was also intended to enhance future intelligence sharing.
At the time of the March report, Agustin was active on Facebook as Hobi Panahan, and listed his current address as Raqqa, Syria.
Hendratno, who lives in Bogor, near Jakarta, reportedly worked as a pilot for VIP airline Premiair until June.
He responded to the leaked report by saying he was only worried about his fellow Muslims and his family.
"I'm only worried about the impact from the news," he said.
"First is criminalising the Muslim image in Indonesia, that's the first thing. The second is about my family."
Indonesian national police chief General Badrodin Haiti said if the men had shown sympathy for Isis on Facebook they hadn't necessarily joined Isis.
"They have sympathy for the Isis struggle, that's what there is," he told reporters.
"From there, the AFP considered them Isis."
Police were working to find out if they were, or had been, in the Middle East, he said.
The AFP report says Hendratno was a pilot for the Indonesian Navy before Garuda and Premiair.
He had posted photos of trips around the world, including to Australia, but by December last year was posting pro-Isis material.
His friends list included many military and commercial pilots.
The report concluded that radicalised pilots were an obvious threat, "as witnessed by past global events" and noted that a recent edition of the al-Qaeda magazine had encouraged aviation attacks.
Both men were trained pilots with contacts in the industry, it said.
The AFP distributed the report to partners in Turkey, Jordan, London, the United States and Europol, The Intercept reported.
The AFP says it doesn't comment on intelligence matters.
Terrorists plots foiled
The United States disrupted an undisclosed number of terrorist plots tied to the Independence Day holiday, highlighting the risk of an attack on American soil inspired by Isis (Islamic State) extremists, FBI director James Comey said.
Comey said that the FBI had arrested at least 10 people in the past four weeks on suspicion they were linked to Isis. Some of those detained had plans involving the holiday weekend, he said, without providing further details.
"I do believe that our work disrupted efforts to kill people, likely in connection with July 4th," Comey said.
Comey's remarks came a day after he warned US lawmakers about the growing threat posed by terrorists and other criminals who communicate over encrypted applications that can't be deciphered.
Dozens of Americans were communicating with Isis over such secretive networks, Comey said yesterday at FBI headquarters.
He said that potential terrorists were "going dark" by using such tools.
FBI officials have said that American sympathisers often follow Isis militants on Twitter and send them direct messages through the social media platform.
- AAP, Washington Post
