|Photo credit Reuters: Romeo Ranoco|
In an interview with the ABC, a senior official from the counter-terrorism body known as the BNPT said some Indonesians had been arrested trying to make it to Marawi, while some had returned home and others had been killed.
The continuing battle to take back the city is focusing the political minds of the region, with Indonesia warning the Islamic State (IS) group could pose a threat elsewhere, like Myanmar.
Barely any militants are thought to be left in Marawi, but the Philippines military has still not taken control of the city.
And there are rising fears other cities could be at risk.
The death toll in Marawi is reportedly nearing 700, among them more than 500 IS-linked militants, as well as hundreds of thousands of residents reported to have been displaced.
Inspector-General Hamidin, deputy of International Cooperation at BNPT, said the threat across the water to Indonesia's north meant a greater threat at home.
"We can see that they keep losing," he said.
"There has been 300 hostages in the mosques and they can't save anyone so far."
The Inspector-General said the problem for Indonesia was not the potential for a similar takeover on Indonesian soil, but that young radical men wanted to join the fighting.
"For those who have returned, we don't have the number yet, but we are sure that several people went there," he said.
"That's the problem for Indonesia — Indonesia won't be used as a base, but Indonesia will be used as a place for recruitment."
There are believed to be about 20 Indonesians fighting in the southern Philippines, but that number has not been confirmed by the Government.
'We need to keep an eye on Myanmar'
Hamidin said the current threat for Indonesia came from the Sulu Sea, where trilateral navy patrols are already underway in the Indonesian, Philippines and Malaysian border areas.
But he warned attentions should also be on the Andaman Sea, and potential Islamic State infiltration in known groups in Myanmar.
"Myanmar has a potential to be a future threat," he said.
He said Indonesia should not confirm any of its citizens had been killed in the fighting in the Philippines until DNA testing has been done.
By Indonesia correspondent Samantha Hawley