Military officials had previously named bodyguards hired by the Ampatuan clan as the suspected gunmen in the massacre.
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, he did not indicate that an arrest was imminent.
Speaking on DZMM radio, Espina said investigators still needed to speak with witnesses before they can secure a court order for the arrest of the suspects, although he insisted authorities would remain impartial.
"We will not treat anyone above the law," Espina said.
Death toll rises
His comments came after police investigating the killings said they had uncovered more bodies, taking the death toll to 46 in what is believed to be the worst politically-linked massacre in the Philippines.
|Arroyo has ordered a state of emergency in the south following the killings [Reuters]
The victims were abducted by gunmen 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 gunmen 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'
|Media groups have called on the government to bring the killers to justice [Reuters]
The unprecedented violence has sent shockwaves through the Philippines and around the world.
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," said Malou Mangahas of the Philippine Centre for Investigative Journalism.
"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".