National Security Adviser Norberto Gonzales said both reports did not categorically state the government is behind the killings or any indication of a state policy that would authorize or justify the murder of suspected communists.
"According to Alston and the Melo Commission, there is no sanction or state policy on the part of the Armed Forces and the government itself to undertake the killings," Gonzales pointed out.
"That is vindication for us and give us more resolve to put an end to this violence," he said.
Gonzales stressed the government has been cleared of the accusations.
The government inquiry, headed by retired Supreme Court justice Jose Melo and made public only after pressure from Alston, said a small group in the military allowed and even encouraged the killing of "enemies of the state."
Alston said last Wednesday the Armed Forces of the Philippines (AFP) was in "almost total denial" about the need to take action on the murders, which have tarnished the Arroyo administration and drawn international criticism.
Press Secretary and Presidential Spokesman Ignacio Bunye said the government will follow the recommendations of the Melo Commission.
The panel recommended the opening of the witness protection program and that a special court be established to try those involved.
"Special courts to try political and media killings are already being established and the witness protection program is being beefed up," Bunye said.
"These cases will be resolved under the rule of law even as government clamps down on election-related violence that has been the bane of our democratic system."
"President Arroyo is determined to end the culture of violence with the same fervor that she has championed the culture of enterprise and productivity," he added.
Gonzales said the Melo Commission, on the extensive study on the issue, has no direct evidence but only circumstantial evidence, linking some elements in the military to the killings.
"There is no official or sanctioned policy on the part of the military or its civilian superiors to resort to what other countries euphemistically call ‘alternative procedures’ meaning illegal liquidations," Gonzales quoted a line in 68-page the report.
But Gonzalez admitted authorities would have work hard to determine the identities of the "small group" within the military the panel had said to be behind the killings.
The human rights group Karapatan claimed more than 800 people have been murdered for political reasons since Mrs., Arroyo took office in 2001.
The AFP, which has been battling the NPA for decades, claimed human rights groups ignore the large numbers of people killed by the communist guerrillas.
The Partido Demokratiko Sosyalista ng Pilipinas (PDSP), on the other hand, said the culture of secrecy in the AFP has somehow contributed to the problem of insurgency.
"The military’s practice of concealing documents has been a setback to the government’s drive to crush communist rebels," Gonzales said as PDSP chairman.
Jesuit priest Father Romeo Intengan, one of the founders of the PDSP, said the military should have declassified earlier to the public all documents and video footage showing some party-list groups and militant organizations are being used as fronts of communist rebels.
He also said the military should show more recent evidence in its possession.
Intengan was reacting to the footage earlier shown by the military where Jose Ma. Sison, founding leader of the Communist Party of the Philippines-National Democratic Front-New People’s Army (CPP-NDF-NPA), identified several groups allied with the communist movement. These were the Bagong Alyansang Makabayan, Kilusang Mayo Uno, Kilusang Magbubukid ng Pilipinas, Gabriela, League of Filipino Students, Alliance of Concerned Teachers, and Kadena.
The video clip has been in the possession of the military for years but it was released only last week.
"The AFP should rethink its policy on the classification of documents. It has difficulty winning the propaganda war against the enemy because it does not give the public vital information that they need to know. The persistence of communist insurgency springs partly from the weak capability of the AFP in promptly providing vital information to the general public," Intengan said.
If the military has more evidence showing the communist tie-up with legal sectoral and party-list groups, Intengan said the military should have declassified these documents and release them to the public.
Intengan, for his part, confirmed six extreme leftist party-list groups were front organizations of communist rebels.
The alliance between the NPA and some party-list groups becomes obvious during elections, he said.
Intengan claimed NPA rebels campaign for their candidates while at the same time, intimidate or harass rival groups.
And yet, the extreme leftist party-list groups have never denounced the violence of the NPAs despite appeals from other sectors.
Evidence of this "bond" is the victory of Bayan Muna, Gabriela and Anakpawis in areas controlled by the NPA.
A careful study of the votes garnered by these three groups showed a clear correlation between the number of votes cast for the party-list groups and the existence of CPP-NPA guerrilla fronts, he said.
Intengan earlier claimed that aside from the militant party-list groups already represented in Congress, communist rebels are also using "emerging party-list groups" as legal fronts.  Paolo Romero