Seven people have been killed in fighting between the Philippine military and Muslim rebels in the country's south, authorities said Thursday, in one of the deadliest clashes since a landmark peace pact was signed in 2014.

The ongoing fighting broke out Tuesday in Basilan island province, off the main southern island of Mindanao, following what the military said was a "miscommunication" between its soldiers and members of the Moro Islamic Liberation Front (MILF).

For decades the Catholic-majority Philippines has been plagued by violent insurgencies, including a Muslim-led separatist uprising that has killed more than 100,000 people.

A peace deal with the MILF, the largest of the rebel groups, was sealed in 2014.

Its leaders now head a self-ruled area in the former battlefields that include Basilan, as the process of disarming the MILF's 40,000 fighters drags on.

Government officials and former rebels who now lead the transitional government in the Bangsamoro Autonomous Region in Muslim Mindanao have expressed concern over the latest clashes.

Presidential peace adviser and former military chief Carlito Galvez said he was "deeply concerned" and efforts were underway on the ground to defuse tensions.

"We cannot allow this latest incident in Basilan to negate the major gains we have achieved over the years," Galvez said in a statement posted on Twitter Thursday.

Chief MILF negotiator Mohagher Iqbal said the flare-up was "unfortunate" and called for an immediate halt in fighting to prevent the situation from "escalating".

The military said fighting erupted after soldiers and local officials went to confront a group of armed members of the MILF seen entering Ulitan village in contravention of the peace agreement.

Brigadier General Domingo Gobway said an MILF rebel shot at the soldiers, igniting clashes.

At least three soldiers and four rebels have been killed, according to separate figures provided by the military and the MILF. Fourteen soldiers and three rebels have been wounded.