Wearing a yellow plastic poncho to protect him from intense rain, Francis delivered an emotional mass to about 200,000 people in the typhoon-ravaged central Philippine city of Tacloban.
However, plans to spend the entire day in Tacloban and nearby areas that were devastated by Super Typhoon Haiyan 14 months ago were ruined by another storm, forcing him to fly back to Manila at lunchtime.
"So I apologise to you all. I'm sad about this, truly saddened," the 78-year-old pontiff told thousands of people who had gathered at one church shortly before he raced back to the airport.
The pope's plane made the 90-minute flight back to the Philippine capital of Manila safely.
But highlighting the dangers of the storm, a papal volunteer at the morning mass died as steel scaffolding collapsed on her, a church spokesman said.
A plane carrying three of President Benigno Aquino's aides then overshot the runway on take-off at Tacloban and nosedived into mud, 30 minutes after Pope Francis's plane flew back to Manila. No-one was badly injured.
Philippine aviation authorities confirmed that the storm's strong crosswinds had blown the plane off the tarmac.
The trip to Tacloban and surrounding areas was one of the top reasons for the pope making a five-day visit to the Philippines, the Catholic Church's Asian stronghold, where he is a highly revered figure.

Haiyan, the most powerful storm ever recorded on land, left 7,350 people dead or missing in November 2013 as it devastated fishing and farming towns that were already among the Philippines' poorest.
The pope celebrated a truncated but still deeply emotional mass for survivors at Tacloban's airport, after receiving a joyous welcome from a crowd that police estimated at about 200,000 people.
"Long live the pope," the crowd chanted as he walked off the plane to be immediately buffeted by strong winds and heavy rain.
His welcome echoed the rapturous reception that millions gave the pontiff during the first two days of his trip to the Philippines.
Most of the people in the crowd at Tacloban wore thin plastic ponchos handed out by organisers, and the pope also put one on before walking on to a nearby stage to celebrate mass in heavy rain.

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