"He saw, and participated in, the killings and could have directly named in court those involved."
Roque warned that Upham's killing, which he was told occurred last week, could potentially weaken the case against the Ampatuan family.
'Worst possible message'
Roque said Upham had been talking to prosecutors in the capital Manila since February, but went back to Maguindanao after the justice department did not act quickly on his request for protection.
"He went back to Maguindanao when it became apparent the witness protection programme would take a while to take him in," Roque said.
US-based Human Rights Watch said the killing raised doubts about the government's resolve in seeing justice done in the case.
"Massacre witnesses are dying while the government sits on its hands," Elaine Pearson, the group's Asia director, said in a statement.
"This sends the worst possible message to other witnesses thinking of coming forward."
Upham's death comes two months after an uncle of another witness was shot and killed in what authorities said was part of a plan to intimidate those speaking out against the Ampatuan clan.
The clan, which has ruled Maguindanao for a decade, enjoyed political ties with outgoing President Gloria Arroyo, who used the family's huge private army as a force against separatist rebels.
Six clan members are among 196 people charged over the murders, allegedly carried out to prevent a member of a rival clan from running as governor of the province.
The main suspect, Andal Ampatuan Jnr, allegedly led about 100 armed men who stopped the convoy of supporters of Esmael Mangudadatu and then summarily executed 57 people, including 30 journalists.
The closely watched trial, which has been suspended since April, has been mired in controversy.
Alberto Agra, the justice secretary in April controversially dropped charges against two Ampatuan suspects, but was forced to reverse his decision after public outrage.
The justice department then courted more criticism when it allowed the main suspect, Ampatuan Jnr, to hold a news ess conference inside his prison cell without handcuffs.
Roque said the court has not yet given prosecutors a definite timeline for the resumption of the trial.
"But justice needs to be served quickly in this case," he said.