He said the US was providing help in forensic tests and that he did not know when the results would be ready.
Former members of Abu Sayyaf who had surrendered helped troops find the site.
They said he had been carried there "dying" after having been shot in the neck, said Caculitan.
"If you look at the terrain... it would not be easy to locate the site without reliable information," he said.
Janjalani, who was thought to have been killed in a clash with Filippino marines in September, was wanted in connection with a series of beheadings, bombings and mass abductions carried out in the Philippines.
US backed offensive
US-backed Philippine troops launched an offensive on southern Jolo island in August, searching for Janjalani and two Indonesian men wanted in connection with the 2002 Bali nightclub bombings that killed over 200 people.
"We are not yet officially confirming that it's him. We are still waiting for the results of the DNA examination"
Lt Col Ariel Caculitan,
Janjalani and other Abu Sayyaf leaders had been charged with several deadly attacks in the Philippines, including a 2004 ferry bombing that killed 116 people.
In May 2001, the Abu Sayyaf abducted three Americans and 17 Filipinos from a resort, starting a yearlong kidnapping spree that eventually involved 102 hostages.
Eighteen of the hostages, including one American, were beheaded or hacked to death.
The abductions sparked an influx of US military counterterrorism trainers.
Abu Sayyaf has said it is fighting to create a Muslim state in the southern Philippines, which has a large Muslim minority.
The military currently estimates the Abu Sayyaf to have about 400 armed men in Jolo and outlying provinces.