The remains were unearthed Tuesday after four Abu Sayyaf bandits surrendered and led the military to the location of the supposed grave site in Barangay Kabuntakas.
The body was wrapped in a Muslim ceremonial burial cloth.
The military, on the other hand, was cautious in making the announcement since Janjalani has been reported killed several times in the past, only to embarrass the government by launching deadly terror attacks.
Brig. Gen. Juancho Sabban, 3rd Marine Brigade Commander based in Jolo, said they are still verifying if the remains are Janjalani’s.
"It is not confirmed yet because we need to be sure by having the skeletal remains investigated through forensic or DNA test," he said.
Sabban said the four Abu Sayyaf surrenderees led them to the grave where Janjalani was supposedly buried, located around two kilometers away from the site of a major encounter last Sept. 4.
Janjalani was earlier reported to have been badly wounded in that clash, which also left five soldiers dead and 20 others wounded.
The four Abu Sayyaf bandits "were the ones who carried him (Janjalani) from the encounter site, to where he was buried," Sabban said.
He said more Abu Sayyaf bandits are expected to surrender following the alleged death of their leader.
"Janjalani is the one binding them together," Sabban said.
Armed Forces of the Philippines (AFP) chief Gen. Hermogenes Esperon also told reporters in Manila that they are still validating the information.
"What is confirmed was that there was a dead body that was exhumed yesterday (Tuesday) in Patikul, Sulu but we could not confirm kung sino iyon (who was it)," Esperon said.
Esperon announced US forensics experts are helping out in working on the DNA samples gathered at the scene to establish whether the body was that of Janjalani.
Esperon said the DNA would be checked against that of Khadaffy’s older brother Hector Janjalani, who was sentenced to life imprisonment two years ago for abducting American Jeffrey Schilling in August 2000.
"Our counterparts, the American forces that are there have also taken a sample (tissue) so that they could make their own DNA tests," Esperon said.
The US Embassy, through Press Attaché Matthew Lussenhop, said the US government was requested to perform the forensic test on the body.
Lussenhop said they are still awaiting the report of the US Federal Bureau of Investigation on the forensic test and DNA results to determine if the body belongs to Janjalani.
"We’re providing assistance because we were requested by Philippine authorities to identify the remains. But the information and announcement on the result of the test will come from Philippine authorities," Lussenhop said.
"But there’s no final determination yet. We’re still awaiting FBI report on the forensic report," he said.
Marine spokesman Lt. Col. Ariel Caculitan said reports that Janjalani had been killed surfaced in September as troops under "Oplan Ultimatum" launched the massive manhunt on Jolo involving more than 5,000 soldiers.
Caculitan, however, would not say why the body was only recovered Tuesday.
Caculitan said former Abu Sayyaf bandits who had surrendered helped troops find the site and claimed Janjalani had been shot in the neck. They said he had been carried "dying from the encounter site" to the burial location two kilometers away.
"If you look at the terrain... it would not be easy to locate the site without reliable information," Caculitan said.
There were also reports that Janjalani died last October after succumbing to infection from a gunshot wound on his right leg during an encounter with troops last Sept. 4.
Marine commandos attacked an encampment of the bandits killing several of them, including Janjalani.
Intelligence reports coming from Panamao town also reported Janjalani was killed during an encounter with the military and his remains were hastily buried.
The Marines cited reports that Janjalani was monitored to be in serious condition seeking refuge in the mountains near Panamao last October.
The bandit leader was reported to be in serious condition as the gunshot wound he sustained had already infected his whole right leg.
But there are also conflicting reports that the decomposing body recovered at the site was that of Jemaah Islamiyah (JI) militant Umar Patek.
The Indonesian militant was also reported as among those who were seriously wounded during the attack.
Sources also added Janjalani is still alive and had produced a video footage on Christmas Day promoting the cause of Islam.
"We are still validating this report by securing a copy (of the video), but so far we have not been successful," an intelligence official said.
The video purportedly showed Janjalani urging for a holy war and calling for the continued fight against enemies of Islam.
Protestant missionary Gracia Burnham told ABS-CBN that she will "anxiously" await confirmation from authorities if the body unearthed by the military is indeed Janjalani.
She said that now that her husband and Janjalani are dead, they are both at the mercy of God, which makes her feel sad for the Abu Sayyaf leader.
Burnham and her husband, Martin, were among those abducted by the bandit group at a posh resort in Palawan in May 2001. The Burnhams were celebrating their 18th wedding anniversary when they were abducted.
The couple was held in captivity for 376 days in Basilan until June 7, 2002, when the military rescued Gracia but failed to save Martin who was killed during the rescue attempt.
She authored a book, "In The Presence Of My Enemies," narrating their experience during captivity.
Esperon, meanwhile, cautioned that Janjalani’s death would not mean the end of the Abu Sayyaf, but was a major setback.
Troops are continuing to hunt down JI militants Patek and Dulmatin, whom Abu Sayyaf bandits are believed to be protecting on the island.
Both men are wanted for the October 2002 night club bombings in Bali, Indonesia, in which 202 mostly foreign tourists were killed.
The JI and Abu Sayyaf are both on the US government’s list of foreign terrorist organizations.
Under Janjalani, the Abu Sayyaf launched kidnapping raids targeting American, European and Asian tourists earlier in the decade.
Two of three American hostages kidnapped in 2001 were killed in captivity.
The US government has offered a five million dollar reward for any information leading to the killing or arrest of Janjalani.
Khadaffy Janjalani took over command of the Abu Sayyaf when his brother, Afghan-trained Islamic firebrand Abubakar Abdurajak Janjalani, who founded the group, was killed in a gunfight with police in December 1998. -With Jaime Laude, Pia Lee-Brago, AP, AFP