Jovito Palparan, dubbed "The Butcher" by leftist groups for his brutal anti-insurgency tactics against communist guerillas, was convicted of kidnapping and handed a minimum term of 20 years by a court in Bulacan province just north of Manila.

Palparan and three other ex-military officers were accused of abducting two female university students in 2006, on the suspicion they were linked to communist groups. The women remain missing.

The court ruled that witness testimonies that the two students were seen in a military camp being tortured were "credible". One witness said the women told him they were raped.

Human rights groups accuse Palparan of being behind the killing of leftists when he was a top military officer battling communist guerrillas in rural areas of the impoverished archipelago, under former President Gloria Arroyo.

"He was one with his men in the desire to stamp out the enemies of the state... who they believe deserve to be erased from the face of the earth at any cost," the court ruling said.

Palparan denied the charges, calling the judge "stupid" as the verdict was read on Monday.

A government commission which investigated political killings said in 2007 that Palparan was a key suspect in murders of people deemed "enemies of the state". He went into hiding in 2011 after being charged in the case of the two activists, but was arrested in 2014.

The military has been accused of carrying out extra-judicial killings of opponents.

The 49-year communist rebellion in the largely Catholic nation is one of Asia's longest-running insurgencies and has claimed 30,000 lives by the government's count.

On Monday, Human Rights Watch said Palparan's conviction dealt a "big blow" to the nation's infamous "culture of impunity" in which powerful figures can commit crimes without fear of punishment.

Cristina Palabay, secretary general of rights group Karapatan, said the conviction was a warning to security officers over President Rodrigo Duterte's war on drugs, which has killed thousands.

"It sends a strong message to men in uniform that they can't do as they please. So with Duterte essentially doing a Palparan 2.0, I fear the possibility of him pardoning (Palparan)," Palabay told AFP.

Duterte's spokesman said the government respected the ruling and wanted justice for the victims.