The extremists fighting under the black banner of the Islamic State (IS) group have remained holed up in pockets of Marawi, weathering daily air and artillery bombardment and deadly urban street battles.
Military spokesman Lieutenant Colonel Jo-ar Herrera said the route was discovered following the arrest of a man who used a boat to smuggle ammunition into the battle zone and ferry wounded militants out.
The military was able to cut off the "logistical and medical highway" across Lake Lanao, he said, adding that boat patrols on the lake have been bolstered.
"This is good news because we have now blocked this highway."
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Marawi, the most important Muslim city in the mainly Catholic Philippines, is located on the shores of Lake Lanao on Mindanao island.
Hundreds of militants attacked the city on May 23.
The government described the attack as a rebellion aimed at setting up an IS province in the area -- part of what it said was an attempt to carve out a caliphate in Southeast Asia.
Nearly 400 people have been killed, including 290 militants and 70 troops, according to official figures. Most of Marawi's 200,000 residents have fled and much of the city is in ruins.
Herrera said the military was still trying to confirm reports that a key leader of the attack, veteran Filipino militant Isnilon Hapilon, had been able to escape the military encirclement.
The militants are also holding around 100 hostages, including a Roman Catholic priest they abducted early in the siege.
Defence Secretary Delfin Lorenzana said Tuesday the military was under pressure to crush the militants before Duterte delivers his annual state-of-the-nation address on July 24.
"There's a bit of pressure because if Marawi is still there and there is still killing, it doesn't look good for the state-of-the nation address by the president," Lorenzana said on radio station DZRH.