Three gunmen on a motorcycle attacked Sotero Llamas, 55, in the town of Tabaco, 550km southeast of Manila.
Chief Superintendent Victor Boco of the regional police said Llamas had been shot in the face and was pronounced dead on arrival at a local hospital.
State prosecutors filed rebellion charges against Llamas earlier this month.
He and 40 other leaders of the communist movement are accused of plotting to topple Gloria Arroyo, the president, in February.
Llamas was a former guerrilla commander in the southeastern Bicol region. He was arrested in 1995 but released a year later.
Military intelligence officials said he was a member of the central committee of the Communist Party of the Philippines and regional commander of the Maoist-led New People's Army (NPA).
He was also a consultant to peace talks between the communist rebels and the government that have been mediated by Norway since 2001.
The government said some rogue lieutenants had met senior NPA leaders in Batangas province south of the capital before Llamas was arrested in February.
Wave of killings
It linked the party leadership with the foiled coup, including rebels living in exile in the Netherlands.
Negotiations to end nearly 40 years of a communist insurgency that has killed 40,000 people stalled in August 2004 when the government refused to try to convince Washington and some Western European states that the rebels should be removed from their list of terrorist organisations.
Llamas emerged from the underground to organise and mobilise rallies and briefly moved into local politics, running and losing the gubernatorial race in his home province, Albay, in the May 2004 elections.
Human rights advocates and left-leaning groups say the government was behind the wave of murders and disappearances of nearly 100 journalists and activists since Arroyo assumed power in 2001.Arroyo's security officials defended the government's rights record, saying the killings could be part of a purge within the communist movement.