The Burnhams were held hostage for more than a year
Philippine President Gloria Macapagal Arroyo has ordered an investigation into allegations by a American woman kidnapped by the Abu Sayyaf rebels that military officials were colluding with her captors.
Gracia Burnham, who was kidnapped in 2001 along with her husband and several others, made the claim in a new book, In the Presence of My Enemies.
In a statement, President Arroyo said she promised justice for the Christian missionary, who was held by the Abu Sayyaf for more than a year.
Gracia Burnham was rescued in June 2002, but during the ill-fated rescue operation, her husband and a Filipino hostage were killed and she herself was injured.
There should never be any form of contact between troops
and terrorists, except armed contact"
In her book, Mrs Burnham said that Filipino soldiers routinely provided the Abu Sayyaf with guns and ammunition during her time in captivity.
She also claimed that an army general gave the rebels food, in an attempt to get a cut of any ransom money.
She said it was army gunfire rather than bullets from the Abu Sayyaf that wounded her and killed her husband.
Mrs Arroyo said she would arrange "a formal and thorough investigation of Mrs Burnham's allegations so
that the facts may be laid bare to the public".
She said the authorities would take action against anyone found culpable of military violations, and added that there "should never be any form of contact between troops
and terrorists, except armed contact".
The Burnhams were celebrating their wedding anniversary in May 2001, when they were kidnapped by the Abu Sayyaf and taken to the island of
The Abu Sayyaf, labelled by both the Philippine Government and the United States as a terrorist organisation, is a Muslim guerrilla group which uses kidnapping and extortion to garner funds.
American troops have been deployed in the Philippines to help the local security forces in their campaign against the rebels.
Ms Arroyo's spokesman, Ignacio Bunye, said on Thursday that the president still had faith in the military offensive against the Abu Sayyaf.
"The sacrifices of our dedicated soldiers should not be tainted
by these accusations," Mr Bunye said.
National Security Adviser Roilo Golez told the BBC's East Asia Today programme: "We have to remember that about 50 members of the military were killed in the operations against the Abu Sayyaf to rescue the Burnhams."