By Agence France-Presse
The attack brings to at least eight the number of people abducted from vessels in the region over the past week, including an elderly German sailor, raising fears authorities are unable to control the worsening piracy problem.
The MV Royal 16 was sailing less than 20 kilometres (12 miles) from Basilan island, a stronghold of Abu Sayyaf militants, when it was attacked on Friday morning.
Two crew members, one of whom was wounded, escaped and were rescued by a local cargo ship in the area, authorities added.
"Sea and naval assets (were) already deployed to search and rescue the said kidnap victims," said regional military spokesman Filemon Tan.
The nationalities of the five crewmen and the identity of the kidnappers were still unknown.
In recent months, the Abu Sayyaf has been accused of kidnapping dozens of Indonesian and Malaysian sailors in waters off the southern Philippines.
On the weekend an Abu Sayyaf commander claimed responsibility for abducting a 70-year-old German sailor and murdering his wife.
In what maritime experts described as a landmark incident, the captain of a South Korean cargo ship and a Filipino crewman were abducted off their vessel, the first such attack on large merchant vessel.
Abu Sayyaf militants this year beheaded two Canadian hostages after demands for millions of dollars were not met. Most of the Indonesian and Malaysian sailors were released after ransoms were reportedly paid.
However two more Indonesian sailors were abducted on November 5.
The Abu Sayyaf is a loose network of militants formed in the 1990s with seed money from Osama bin Laden's Al-Qaeda network, and has earned millions of dollars from kidnappings-for-ransom.
Philippine President Rodrigo Duterte has launched a military offensive to "destroy" the Abu Sayyaf.
But the militants have defied more than a decade of US-backed similar offensives, surviving in their mountainous and jungle-clad southern island strongholds where they have support from local Muslim communities.
The Abu Sayyaf is not the only threat with those near-lawless islands home to other armed gangs and people whose families have been involved in piracy for generations, according to security analysts.
The Philippines has agreed to allow Malaysian and Indonesian maritime forces to pursue kidnappers into its waters to contain the threat, Malaysian Prime Minister Najib Razak said on Thursday.