On Tuesday, Arroyo vowed an all-out effort to bring those responsible for the killings to justice, saying that no-one would be seen to be above the law.
She has declared a state of emergency in Maguindanao and a neighbouring province, ordering hundreds of extra troops to the area.
Military officials had previously named bodyguards hired by the Ampatuan clan as the suspected gunmen in the massacre.
"We will not treat anyone above the law"
Philippines police spokesman
But on Wednesday a Philippine police spokesman singled out Ampatuan Jr as the lead suspect for the first time.
"According to the initial reports, those who were abducted and murdered… were initially stopped by a group led by the mayor of Datu Unsay," Leonardo Espina, the chief superintendent, said.
Nonetheless, Espina did not indicate that an arrest was imminent.
Speaking on DZMM radio, he said investigators still needed to speak to witnesses before they can secure a court order for the arrest of suspects, although he insisted that the authorities would remain impartial.
"We will not treat anyone above the law," Espina said.
But Al Jazeera's correspondent Marga Ortigas, reporting from the scene of the massacre, said those assurances would likely do little to calm nerves in the region where many locals said they feared retaliatory attacks.
She said many people were upset that the police had not arrested or at least brought in for questioning any of the main suspects.
"There isn't much faith in the government ... because the family that is believed to be behind it is a very close ally of president Arroyo, and the fear is that if anything they will only help provide cover or whitewash the entire attrocity," Ortigas said.
"Authorities don't know how to conduct the autopsies yet, because the intial investigations at the site haven't really ended.
"Many of the victims are unidentifiable until possible DNA testing takes place," she said.
Officials said many of the dead were hard to identify because they had been shot at close range with M16 rifles, destroying their facial features.
Police have said they expect to find more victims as they continue to excavate the area of the massacre.
|Arroyo has ordered a state of emergency in the south following the killings [Reuters]
The victims were abducted on Monday as they were travelling in a convoy to nominate Esmael Mangudadatu as the opposition candidate for governor in elections due to be held next year.
The dead include 18 Filipino journalists from regional newspapers, TV and radio stations who were accompanying Mangudadatu's relatives and supporters to file his nomination papers.
Some of the victims had been buried in a mass grave, while others were dumped beside a road.
Mangudadatu, the gubernatorial candidate, was not himself in the convoy because he had received death threats.
On Tuesday, he pressed the Philippines defence secretary, national police chief and military commanders to immediately arrest and prosecute those behind the killings.
Mangudadatu said four witnesses in his protection had told him the convoy was stopped by armed men loyal to Ampatuan Jr, to prevent his family from filing election papers.
"It was really planned because they had already dug a huge hole [for the bodies]," Mangudadatu said.
He said there were reports from the area that the militia had been blocking the road for a few days.
'Moved to tears'
The unprecedented violence has sent shockwaves through the Philippines and around the world.
|Media groups have called on the government to bring the killers to justice [Reuters]
On Tuesday evening, a group of journalists joined a march in the capital Manila calling on the government to conduct a speedy investigation into the killings.
"We cannot ignore the killings of journalists anymore," Malou Mangahas of the Philippine Centre for Investigative Journalism said.
"I am sure all of us yesterday were really appalled, moved to tears, especially those who know, or who knew those who had fallen."
Paris-based media watchdog Reporters Without Borders said the deaths of the 18 reporters was "the largest single massacre of journalists ever".
In New York, Ban Ki-moon, the UN secretary-general, condemned what he said was a "heinous crime committed in the context of a local election campaign".
In a statement delivered by a spokeswoman, Ban said he hoped that "no effort will be spared to bring justice and to hold the perpetrators accountable".