The state weather service said the eye of Tropical Storm Wukong is expected to hit land on Samar island before dawn on Wednesday, bringing "heavy to intense" rain over a 350-kilometre-wide front.
These areas should expect potential landslides and floods, and local officials may have to order evacuations, said civil defence chief, Benito Ramos.
Mr Ramos said the outer bands of the storm, which has gusts of up to 80 kilometres an hour, would affect areas of the south devastated by Typhoon Bopha earlier this month.
"This will cause flash floods and landslides. Our people still have time to evacuate, but we give the local government units the discretion to make the call," he told reporters.
No evacuations have been reported so far.
Those families affected by Typhoon Bopha are relying on donations for food and are staying in temporary shelters, as they slowly get back on their feet.
The most intense storm to hit the disaster-prone Philippines this year wiped out communities near the coast in the southern provinces of Davao Oriental and Compostela Valley, leaving 1,067 people dead and 834 missing.
More than 6 million people across rural and coastal provinces were affected by the storm.
Tens of thousands of houses were totally wrecked, coconut farms and banana plantations were levelled, destroying livelihood, and inland villages were isolated as road networks were badly damaged.
In the town of Cateel in Davao Oriental, where more than 150 people were killed in the typhoon, survivors held traditional dawn masses, which are done for nine consecutive days leading up to Christmas Eve.
A predominantly Catholic nation, the Philippines is big on Christmas celebrations, when families get together, throw parties and exchange presents.
In Davao Oriental, the mood is more sombre, not helped by rains from a low pressure area, but villagers have kept alive the holiday spirit.
"We're still thankful, even if we only have the chapel as the last structure remaining. We are okay, as long as the people's hearts are still directed towards the Lord," said villager Elena Ravelo.
In Compostela Valley, survivors will be spending the holidays in tents, as they await aid for construction materials to rebuild their homes.
Relief has been trickling in from international aid groups and donors including the United States, Australia, and most recently, Brunei, China and New Zealand.
"People have been very deeply affected. Their houses have been destroyed, in some barangays (villages), completely, everything is down. The livelihood is gravely affected as well because the cultures (farming), the trees, everything is down," said Sebastian Bourgoin from the International Committee of the Red Cross.
More than 600 lives were lost in Compostela Valley, and survivors count themselves lucky that they were spared.
"Even if we are facing this difficult situation, we still need to pray. We are still celebrating Christmas. And we are still grateful that we are still alive," said Alejandro Tabino, shortly before he led choir in singing Christmas carols.
About 20 typhoons hit the Philippines every year, often causing death and destruction. Communities have been alerted to a low pressure area, which could bring more rains and trigger flash floods and landslides over the next few days.