"We are calling upon the international community to intercede," he said. "We still believe that the best situation is going back to the peace process."
The warning follows a recent spate of violence which effectively ended a ceasefire and put paid to a peace deal between the Philippine government and fighters in the volatile Muslim-majority region last month.
No terror ties
In the interview, Ebrahim also rejected accusations from some intelligence agencies that the MILF had ties with the al-Qaeda international "terror" network led by Osama bin Laden.
"We have been consistently accused of this and we have consistently also denied having any connection with the al-Qaeda and with the JI [Jemaah Islamiyah]," he said.
He, however, added that because of the war situation in Mindanao anyone could come in as "there is no control of the area".
The MILF chairman said the group was very thankful to the international community for supporting the peace process, saying they believed that peace can be achieved both on the negotiating table and on the ground.
Amina Rasul, director of the Philippine Council on Islam and Democracy, which plays a big role in Philippine Muslim civil society, said the group was "extremely worried" that the conflict will escalate and called on the United Nations and other international bodies to push for a return to negotiations.
Speaking to Al Jazeera from Manila she said that even before talks broke down there were reports that both sides were reinforcing troops, and that the recent kidnappings of aid and development workers had only added pressure to an already tense situation.
|Intense fighting has displaced more than half a million people
In the latest violence on Wednesday, MILF fighters attacked an army patrol in the town of Calanugas, killing seven soldiers and at least one rebel fighter, according to Philippine military officials.
Hours later they attacked an army outpost in the same town, wounding five soldiers and taking an undetermined number of casualties, Colonel Rey Ardo, the local commander, said.
In another clash on the same day, MILF fighters ambushed troops escorting labourers to a road project.
Colonel Dickson Hermoso, a local government commander, said two soldiers were wounded in the attack.
Negotiations between the government and the MILF, which wants an expanded Muslim area in the Mindanao region, broke down last month.
The parties were supposed to sign the peace deal on August 5, creating an ancestral homeland for four million Muslims.
But the deal on the size of a Muslim homeland and a future government's powers failed following protests by local Roman Catholic politicians and community leaders.
Since then, about 100 civilians have been killed and more than half a million people have lost their homes and livelihoods, creating a growing refugee crisis.
According to the International Committee of the Red Cross the fighting has reached its worst level in five years.