The gunmen have mustered a force of about 200 fighters and fought a series of skirmishes with the security forces this year after government forces retook Marawi last October, Colonel Romeo Brawner told AFP.
"They have not abandoned their objective to create a caliphate in Southeast Asia," said Brawner, the commander of a Marawi-based military task force.
"Mindanao is the most fertile ground," he said, referring to the country's southern region.
Struggling with widespread poverty and armed Muslim insurgencies seeking independence or self-rule, Mindanao must improve poor supervision of Islamic schools or madrasas where most young gunmen are recruited, he added.
He said the armed forces are retooling to meet the challenge of the Maute group, which occupied Marawi over five months and has pledged allegiance to the Middle East-based Islamic State group.
Gunmen who escaped during the early days of the US-backed operation to recapture Marawi are leading the recruitment effort, flush with cash, guns and jewellery looted from the city's banks and private homes, Brawner said.
The recruits are mostly locals, but an unspecified number of Indonesians, some with bomb-making skills, have recently arrived there, he said.
Mindanao military officials said the Maute gunmen murdered three traders in the town of Piagapo, near Marawi, in November last year.
Three jihadists were killed in Pantar, another neighbouring town, on February 8, while three of the Piagapo merchants' suspected killers were arrested in that town last month.
The military also reported skirmishes with the Maute gunmen in the towns of Masiu and Pagayawan near Marawi last month.
The renewed fighting came after President Rodrigo Duterte and other political leaders in the Mindanao region warned of a potential repeat of the siege of Marawi which claimed more than 1,100 lives.
Duterte has imposed martial law over Mindanao until the end of the year to curb the militants' challenge.
Ebrahim Murad, head of the Philippines' main Muslim rebel group the Moro Islamic Liberation Front, which signed a peace treaty with Manila in 2014, also warned Tuesday that jihadists were recruiting and could seize another Filipino city.