Schools and businesses across the capital were shut on Monday as clouds of ash from the Taal volcano drifted over the city.
Seismologists warned an eruption could happen at any time and could potentially send a tsunami surging across Taal Lake, which surrounds the crater.
No deaths were reported, but a truck skidded out of control on an ash-blanketed road, killing the driver and injuring three people in Laguna province. Police said the accident may have been linked to slippery conditions.
More than 30,000 villagers have been evacuated from their homes in the ash-blanketed province of Batangas and nearby Cavite province and officials expect the numbers to rise.
“The speed of escalation of Taal’s volcanic activity caught us by surprise,” Maria Antonia Bornas, chief science research specialist at the Philippine Institute of Volcanology and Seismology, said.
“We have detected magma. It’s still deep, it hasn’t reached the surface. We still can expect a hazardous eruption any time.”
Some residents could not flee their villages because of a lack of transportation and poor visibility, which others refused to leave their homes and farms.
“We have a problem – our people are panicking due to the volcano because they want to save their livelihood, their pigs and herds of cows,” Mayor Wilson Maralit of the town of Balete told DZMM radio. “We’re trying to stop them from returning and warning that the volcano can explode again any time and hit them.”
Mr Maralit, whose town lies along the shoreline of Taal Lake, which surrounds the erupting volcano, appealed for troops and more police to stop people from sneaking back to their villages.
Clouds of ash forced the shutdown of the country’s main airport in Manila on Sunday, with more than 500 flights cancelled. The airport partially reopened on Monday.
A plane carrying Rodrigo Duterte, the Philippines’ president, was later able to land in Manila from his hometown of Davao, his spokesman said, adding he saw the extent of the disaster from the plane.
Volcano Taal sprang back to life on Sunday, blasting steam, ash and pebbles 10 to 15km into the sky, according to the Philippine Institute of Volcanology and Seismology.
On Monday, the ash and steam column reached a height of 2km, with red-hot lava columns reaching less than half of that height.
Frequent tremors and a buildup of pressure of the 1,020ft volcano however, indicated a major and much more dangerous eruption could still happen, said Renato Solidum, who heads the institute.
The government volcano monitoring agency raised the danger level around Taal three notches on Sunday to Level 4, indicating a hazardous eruption within hours to days was possible. Level 5, the highest, means such an eruption is underway.
The volcano’s last disastrous eruption happened in 1965, when more than 200 people were killed.
Taal, one of the world’s smallest volcanoes, is regarded as one of the most active volcanoes in the Philippines, which sits along the Pacific “Ring of Fire,” a region prone to earthquakes and volcanic eruptions.
Additional reporting by agencies