Mitag weakened on Tuesday as it left the Philippines heading for southern Japan, but provinces in the north of Luzon island continued to be battered by strong winds and rain.
Meanwhile, a separate storm, Hagibis, which killed 13 people last week in its initial pass over the Philippines before heading towards Vietnam, reversed its course on Monday to head back to the Philippine islands of Palawan and Mindoro.
The storms return brought heavy rain to the west of the country and forecasters expected it to continue moving in an east-northeast direction across the country over the next 48 hours.
In addition the weather bureau said a third storm was expected to hit the country in the next four days and bring more rain to the eastern part of Luzon and the central Philippines.
The warning comes as air force search and resuce teams continued to search for a reconnaissance jet and its two pilots that went missing on Monday.
The aircraft had been on a mission to locate a fishing boat that sank with its crew of at least 26 near the Spratly islands in the South China sea last week, the air force said.