Security forces have engaged in ferocious street to street combat and launched airstrikes in their efforts to expel the fighters from the city of Marawi, in a conflict that has raised fears that IS is looking to establish a Southeast Asian base in the Philippines.
The military said it had captured the militants' control centre in a deadly battle that began Saturday in a mosque and another building.
"This enormous (military) gain further weakened the terrorist group by denying them their erstwhile command and control hub," military chief General Eduardo Ano said in a statement.
Hundreds of armed extremists flying the black flag of the Islamic State movement in the Middle East occupied Marawi, the Islamic capital of the mainly Catholic Philippines, on May 23.
More than 800 militants, government troops and civilians have since been killed in the conflict, which has forced thousands to flee their homes and destroyed large parts of the once-bustling city.
President Rodrigo Duterte has deployed thousands of troops and imposed martial law across the southern third of the country to deal with the crisis, while the military has launched a US-backed air campaign against the militants.