Director Marcelo Ele Jr., head of the police Anti-Illegal Drugs Special Operations Task Force (AID-SOTF) identified the arrested suspects as Wilhem Papa, Angelito Estores and Manuel Baroga.
Papa is a crewman of the German-registered Xingang while Estores and Baroga are security guards manning the gate of South Harbors Pier 4.
Ele said combined elements of AID-SOTF, Manila Police District, Coast Guard and Bureau of Customs arrived at Pier 4 shortly after midnight.
Customs Commissioner Alexander Arevalo said their Pier and Inspection Division (PID) received reports that marijuana leaves were being loaded into a ship that came from Indonesia.
PID chief Gerry Macatangay immediately sought the help of the Coast Guard, who provided agents with a cutter to intercept the vessel.
"This is the result of close coordination between government agencies in the campaign against illegal shipments," Arevalo said.
At least five traveling bags were being loaded from a banca when the agents announced the raid at 12:22 a.m.
Superintendent Arnold Aguilar, head of the Special Operations Group of AID-SOTF, said someone cut the rope being used to hoist the bags, which then plunged into Manila Bay.
Aguilar said one traveling bag, containing a total of 46.535 kilos of dried marijuana leaves, was in the possession of Papa. The suspect later led government agents to Estores and Baroga, both of the South Port Security and Protection Agency.
The three were turned over to the custody of the Philippine Drug Enforcement Agency.
"We are digging deeper into the syndicates operation abroad so we can provide our foreign counterparts with vital information," Aguilar said.
Aguilar said a kilo of marijuana sells for P20,000.
The AID-SOTF official said the Xingang arrived in the country last Wednesday night from the port of Suraya in Indonesia to unload cargo. It was scheduled to leave for Singapore today before proceeding to the port of Hamburg in Germany.
Initial investigation showed that the ships other crew members were not aware of the syndicates illegal operations, one AIDSOTF official said.