Aquino ordered a coast guard patrol vessel and a fisheries bureau survey ship out of Scarborough Shoal in the South China Sea on Friday night, Foreign Secretary Albert del Rosario said.
“Last night, President Aquino ordered both of our ships to return to port due to increasing bad weather,” del Rosario said in a statement.
“When weather improves, a re-evaluation will be made,” he added.
The announcement was made as Typhoon Guchol approached the country’s north from the Pacific Ocean.
The Filipino vessels have been around the shoal claimed by both countries since April.
A larger number of Chinese maritime patrol vessels as well as fishing boats are also in the area, according to the Philippine side, though both sides imposed unilateral fishing bans in the area during the dispute.
The dispute began after Chinese government vessels blocked Philippine ships from arresting Chinese fishermen near the shoal on April 10.
Since then, both countries have maintained ships there to press their respective claims to the area.
China claims nearly all of the South China Sea, even waters close to the coasts of neighbouring countries. The Philippines and Vietnam have in recent years accused China of becoming increasingly aggressive in staking its claim.