Malaysias The Star newspaper quoted Army field commander Lt. Gen. Masood Zainal Abidin as saying that there was "possibly going to be a spillover of the Abu Sayyaf group," and that authorities were monitoring the situation.
"We are well aware of whats happening on the other side," Abidin was quoted as saying.
Abidin noted the pronouncement made by the Philippine government confirming the death of Abu Sayyaf chieftain Khadaffy Janjalani and bandit group spokesman Abu Solaiman.
"There will be a new (Abu Sayyaf) leader. Its just like a plant, which will see its plant growing when broken," Abidin said.
Armed Forces of the Philippines (AFP) chief Gen. Hermogenes Esperon Jr. said the offensive against the group would be "faster and more ferocious" following the deaths of Janjalani and Solaiman.
"Well give them no quarter," Esperon said. "We have to hit all the remaining leaders while theyre in a crisis."
The government sustained the offensive to run down the Abu Sayyaf following the deaths of its two leaders.
The fighting is taking place in southern Philippines, on the island of Jolo of the Sulu archipelago near the coastline of Sabah on Borneo island.
Up to half a million Filipinos live in Malaysia, many of them families of refugees who fled the separatist rebellion in Mindanao in the 1970s.
The Philippine government has estimated that up to 200,000 Filipinos are living in Malaysia illegally, mostly in Sabah.
The Philippine Coast Guard, for its part, has intensified security measures for possible retaliatory attacks from the Abu Sayyaf striking seaports anywhere in the country.
"We are always ready and have been performing anti-terrorist measures like deployment of sea marshals and regular checking of passengers and cargo in tandem with private sectors. As always, were ready to respond to any specific situation of threats in the maritime transportation," Coast Guard Commandant Vice Admiral Damian Carlos said.
The Moro Islamic Liberation Front (MILF), for its part, said they are helping the Philippine government monitor activities of the Abu Sayyaf for possible retaliatory attacks.
MILF spokesman Eid Kabalu said they are keeping their part of the security arrangement with the government to flush out criminals and terrorists in areas covered by the three-year ceasefire. The MILF is currently in peace negotiations with the Philippine government sponsored by Kuala Lumpur.
Kabalu said the MILF will deny the Abu Sayyaf any sanctuary in their areas.
At the same time, MILF leaders advised the remaining bandit group members to "change their ways and toe the line of legitimate revolutionary organizations that fight for the legitimate grievances of the people."
Khaled Musa, MILF deputy chairman of the committee on information, told the remaining Abu Sayyaf members to follow the holy guidelines of Islam to make amends and change their ways by not harming the people.
Musa said the Abu Sayyaf should be made responsible for the crimes it committed against the people.
"Such a movement (the Abu Sayyaf) has no legitimate cause to fight for and, thus, will soon kiss the face of death," Musa said in a statement posted at their website, www.luwaran.com.
Janjalani and his key commanders have been accused of several deadly attacks in the Philippines, including a 2004 bombing that gutted a ferry, killing 116 people in one of Southeast Asias worst terrorist strikes.
The group gained international notoriety in carrying out mass kidnappings, including the abduction of 17 Filipinos and three American tourists - missionary couple Martin and Gracia Burnham and Guillermo Sobero - from a resort in Palawan in May 2001. AFP, AP, John Unson, Edith Regalado, Edu Punay, Sandy Araneta