"We maintain the Ampatuans are the suspects," Brawner told the AFP news agency.
The military said 22 bodies - most female, some beheaded and mutilated - had been found in a mass grave in a remote mountainous area and the number was likely to rise as soldiers dug further at the site.
Gloria Macapagal Arroyo, the Philippine president, condemned the violence and ordered her top security officials to "personally oversee military action" against those behind the killings.
"No effort will be spared to bring justice to the victims and hold the perpetrators accountable to the full limit of the law," she said in a statement. "Civilised society has no place for this kind of violence."
But Al Jazeera's Marga Ortigas, reporting from the Philippines, said Ampatuan is known to be closely-associated to the government and a close ally of Arroyo so people are watching to see what action the government will take.
Ampatuan is seen to have delivered the votes that swung the 2004 elections in Arroyo's favour, so people in the province fear he may not be punished if he is found to be behind the killings, our correspondent said.
Meanwhile Mangudadatu, whose family members, including his wife, were among those killed according to the military, told local radio that at least four people had survived the attack.
He said the survivors were safe under his care and "will come out at the right time".
On Monday Mangudadatu told local television network ABS-CBN that he had been warned about the dangers of standing for the governorship against Ampatuan, the incumbent and the head of a powerful rival family.
Mangudadatu said he stayed behind in the capital Manila and sent his wife, Genalyn Tiamzon-Mangudadatu, to file his nomination in Maguindanao on his behalf.
Officials said about 100 gunmen stopped members of the Mangudadatu family, lawyers and about a dozen local journalists on a highway on Monday and herded about 40 people away at gunpoint.
The southern Philippines is riven by clan rivalries, including one between the Mangudadatus and the Ampatuans.
Explaining that the area is home to three different insurgent movements, our correspondent said Maguindanao is one of the most politically tense provinces in the country.
The governor position is hotly contested because it is the seat of the autonomous region of Muslim Mindanao, she added.
"The wanton killing of so many people makes this an assault on the very fabric of the country's democracy"
Bob Dietz, Committee to Protect Journalists
Many politicians and elected officials in the region maintain well-equipped private armies.
Leila de Lima, a former election lawyer who now chairs the Commission on Human Rights in the Philippines, told Al Jazeera that the killings showed a "breakdown of law and order" in the area.
"Those politicians who are reported to be behind this, these are the gods in the area, they feel untouchable, they think and act like they're above the law. All these years they have been tolerated," she said.
"We're calling on the national authorities, including the executive department and the police, to do something swift and decisive to avert further violence and to obviate the impression that the situation might get out of control.
"We need decisive action this time. We cannot afford to have such a continuing environment and culture of impunity."
Human rights and journalist groups condemned the killings.
Several newspapers and radio stations have not been able to reach any of about a dozen journalists who were part of Monday's convoy that was stopped at gunpoint.
Paris-based Reporters Without Borders said that if the journalists were killed, the incident would be the "largest single massacre of journalists ever".
"Covering the news has always been dangerous in the Philippines, but the wanton killing of so many people makes this an assault on the very fabric of the country's democracy," said Bob Dietz, Asia programme co-ordinator for the Committee to Protect Journalists in New York.