"Our troops discovered the vehicles and around the vehicles were the scattered bodies of the 21 victims, but we believe there were about 43 to 46 people in the convoy so right now we are looking for the other bodies."
Armed men had earlier seized members of a convoy, among them the wife of Esmael Mangudadatu, a local mayor, his aides, supporters and journalists.
"This is a gruesome massacre of civilians unequalled in recent history"
Jess Dureza, the Philippines president's adviser in Mindanao
Mangudadatu said his wife called him by mobile phone shortly before she and her entourage were abducted.
"She said ... they were stopped by 100 uniformed armed men ... then her line got cut off," he said.
Military officials said Mangudadatu's wife was among the dead.
The convoy was heading to a local elections office to file Mangudadatu's candidacy for governorship of the predominantly Muslim Maguindanao province in the autonomous Mindanao region when they were abducted.
In earlier news reports, Brawner said that the attackers had links to Andal Ampatuan, Maguindanao's incumbent governor, who is said to be embroiled in a family feud with the Mangudadatus.
He said that the abductions were carried out by armed men, most of whom were deputised as government guards by Ampatuan's family and that the leader of the group that staged the kidnapping was one of Ampatuan's sons.
But speaking to Al Jazeera, Brawner acknowledged there was a feud between the two families, but said the army was not in a position to say who had carried out the killings.
"The rightful agency who will pinpoint the suspects will of course be the Philippines national police," he said.
"As far as the armed forces of the Philippines is concerned, we are now securing the area and we are continuing our recovery operations."
Ampatuan, who has been elected as governor three times previously, was not immediately reachable for comment.
Marga Ortigas, Al Jazeera's correspondent in the Philippines, said the families were known to be political rivals.
"This particular governor position is hotly contested because it is the seat of the autonomous region of Muslim Mindanao and the incumbent has been there for years."
Ortigas noted that Maguindanao was one of the most politically tense provinces in the country.
"It is the site of three different armed insurgent movements," she said.
"Elections in the Philippines over the last few years are becoming more and more violent, particularly in this area."
The Philippine government expressed outrage and vowed justice following the killings.
"This is a gruesome massacre of civilians unequalled in recent history," Jess Dureza, the Philippines president's adviser on Mindanao, said.
"There must be a total stop to this senseless violence. I strongly recommend that a state of emergency be imposed in the area and everyone be disarmed. Anything less will not work," Dureza said.
The National Union of Journalists of the Philippines said media organisations had been unable to contact the 10 journalists travelling with the convoy leading them to conclude they were among the dead.
"Never in the history of journalism have the news media suffered such a heavy loss of life in one day," Paris-based media watchdog Reporters Without Borders said in a statement.
"The frenzied violence of thugs working for corrupt politicians has resulted in an incomprehensible bloodshed," it said.