Zulkifli, also known by his alias Marwan, is believed to be hiding in Mindanao and training Abu Sayyaf militants in bomb making.
Washington had earlier included Zulkifli in its most wanted list, placing a bounty of $5 million on his head.
Local police and military officials believe that Zulkifli, a US-trained "engineer blamed for the recent spate of bombings in the country, is suspected to be hiding in Sulu, an Abu Sayyaf stronghold.
Col. David Maxwell, of US Joint Special Operations Task Force-Philippines, said their forces in Sulu are assisting the Philippine military in tracking down Zulkifli.
"We share all our information with the Philippine military and we work together with them," Maxwell told a pool of newsmen here without giving specific details. "We will work hard to support the Philippine security forces in all their operations against terrorism."
The US State Department has offered a $5-million reward for information that will lead to the arrest of Zulkifli, who is believed to have been hiding in the Philippines since 2003.
Zulkifli, born in the Malaysian state of Muar Johor, is allegedly the leader of the Kumpulun Mujahidin Malaysia (KMM) terrorist organization and a member of the JI’s "Markaziyah" (central command).
About 7,000 Filipino troops are also hunting down JI leaders Dulmatin and Umar Patek, who both eluded a military raid last Monday in Talipao along with Abu Sayyaf leader Isnilon Hapilon.
However, three of their followers were captured by elite forces of the army’s Light Reaction Company and Military Intelligence Group 9.
Meanwhile, a huge US force is expected to arrive within the next week in this southern port city and will be deployed in Jolo, according to Maxwell.
The new batch of American soldiers is part of a routine rotation of forces in Zamboanga and Sulu.
"US forces are going to be conducting a normal, routine rotation of forces over the next few weeks, and forces will be coming from the US, arriving here in Zamboanga and going to Jolo, Sulu," he told reporters.
Mindful of the local sensitivity over US involvement in the south, Maxwell stressed that there would be no increase in US troop presence and the new arrivals will only replace troops in Sulu.
"It is just this time many of our soldiers happen to be leaving and changing around at the same time. The same number of forces will arrive and the same number of forces will leave and there will be no change in the number of forces that will be here," Maxwell said.
US troop movements are normally not announced publicly for security reasons, Maxwell added.
"We need to be transparent to erase doubts," he said. A number of US Navy ships are also coming and humanitarian missions for local residents will be held this summer.