Zulkifli bin Abdul Hir, alias Marwan, a Malaysian bomb maker with a $5-million US-government bounty on his head, is roaming the southern Philippines, senior military officials said.
"He is alive and we continue to monitor him," Lieutenant Colonel Ramon Zagala told AFP.
Philippine military chiefs said in February 2012 that Zulkifli was among 15 members of the Al-Qaeda-linked Abu Sayyaf and Jemaah Islamiyah organisations killed in an airstrike on the southern island of Jolo.
Zulkifli is regarded as an expert bomb maker and a senior leader of Jemaah Islamiyah who first went into hiding in the southern Philippines in 2003.
In 2007 the US government offered a $5-million reward for his capture, making him one of the United States' most-wanted men.
Another top Jemaah Islamiyah member, Singaporean Mohammad Ali, alias Muawiyah, was also declared killed in the airstrike, along with a Filipino leader of the Abu Sayyaf.
"This is a big victory. There were three senior leaders (killed). This will have a very big impact on the capability of the terrorists," then-regional military commander Major General Noel Coballes said at the time.
Shortly afterwards, Malaysia expressed doubts about the purported killings but the Philippines' then military spokesman insisted all three were dead.
"Yes, its an A-1 (information). We have something but we cannot divulge all the other information because its an operational (secret)," Arnulfo Burgos, Zagala's predecessor, said at the time.
However Zagala insisted on Wednesday that the Philippine military had never said Zulkifli had definitely been killed.
"There were reports that said he was dead but it was never validated... we never confirmed he was dead," he told AFP.
Zagala declined to answer further questions about the case, such as whether the other two top militants were also alive.
Military intelligence chief Major General Eduardo Ano said there were "consistent reports" Zulkifli was in the strife-torn Cotabato area of the main southern island of Mindanao.
He said Zulkifli was believed to be in contact there with the Bangsamoro Islamic Freedom Fighters (BIFF), a small band of Islamic militants fighting for an independent Muslim homeland in the south.
He said there were 10 to 12 foreign Jemaah Islamiyah members in the southern Philippines, and that Zulkifli was "the most prominent" of them.
The Abu Sayyaf is blamed for the worst terrorist attacks in the Philippines, including the bombing of a ferry in Manila that killed more than 100 people.
They are also accused of carrying out dozens of kidnappings in the remote, Muslim-populated south.
Jemaah Islamiyah wants to set up an Islamic state across Southeast Asia.
It is accused of carrying out many deadly attacks in the region, including the bombing of tourist spots on the Indonesian island of Bali in 2002 that killed 202 people, among them 88 Australians.
At the time of the purported airstrike, a rotating force of about 600 US Special Forces was stationed in the southern Philippines to help train local troops how to combat Islamic militants.
The Philippine military said then that it launched the airstrike with the help of US intelligence.