Francis cut short his trip to a central Philippine island, which he was visiting to meet with survivors of a catastrophic typhoon that killed thousands in the area 14 months ago, because of the storm.
The scaffolding hit the 21-year-old woman in the chest and pinned her to the ground, killing her, Father Amadeo Alvero, spokesperson for the Archdiocese of Palo, told reporters.
He said she was one of many volunteers helping at the mass the pope had given earlier in the day at Tacloban airport, which police said attracted a crowd of about 200,000 people.
An average of 20 tropical storms or typhoons hit the Philippines each year and Mekkhala is the first of 2015.