Two bombs minutes apart tore through a Roman Catholic cathedral on a southern Philippine island where Muslim militants are active, killing at least 20 people and wounding 81 others during a Sunday Mass, officials said.

The attack comes days after a regional vote for a new Muslim autonomous region. Police said at least 20 people died and 81 were wounded, correcting an earlier toll due to double counting. The fatalities included 15 civilians and five troops. Among the wounded were 14 troops, two police and 65 civilians.

The first blast occurred inside the Catholic church on war-torn Jolo on Sunday morning as Mass was being celebrated, and was followed by a second explosion in the parking lot as troops responded, regional military spokesman Lieutenant Colonel Gerry Besana told AFP.

Witnesses said the first blast inside the Jolo cathedral sent churchgoers, some of them wounded, to stampede out of the main door. Army troops and police posted outside were rushing in when the second bomb went off about one minute later near the main entrance, causing more deaths and injuries. The military was checking a report that the second explosive device may have been attached to a parked motorcycle.

Photos issued by the regional police showed debris scattered near the church's entrance and a damaged military truck with a broken windshield.

"The motive is surely ... terrorism. These are people who do not want peace," Besana said.

"We will use the full force of the law to bring to justice the perpetrators behind this incident," Defence Secretary Delfin Lorenzana said in a statement.

The military said it airlifted some of the wounded to the nearby city of Zamboanga for medical treatment.

Jolo lies in the proposed Bangsamoro Muslim-majority autonomous region, which local voters overwhelmingly approved last week.

The island is also a base of the Islamist militant group Abu Sayyaf, which is blamed for deadly bombings, including an attack on a ferry in Manila Bay in 2004 that claimed 116 lives in the country's deadliest terror assault.

Last week voters decisively approved a more powerful autonomous region in the Philippines' south, which is hoped will bring peace and development after decades of fighting that have killed thousands and mired the area in poverty.

Sulu province — which includes Jolo — voted against the creation of the new region, with its governor questioning the law establishing the area before the Supreme Court.

Despite Sulu's vote, legislation provides that the province will still be included in the new political entity as voters from across the current autonomous region voted in favour of it on the whole.

Sunday's bombing comes after a New Year's Eve blast in the southern Philippine city of Cotabato killed two people and wounded 35 others.

Cotabato last week voted to be included in the new autonomous region.