Adelir Antonio de Carli, 41, was attempting to break a record 19-hour balloon flight to raise money for a spiritual rest stop for truck drivers in Paranagua, one of Brazil's main ports.
De Carli, who is an experienced skydiver, began his bizarre journey on Monday afternoon. Wearing a helmet, thermal suit and a parachute, he lifted off from Paranagua on a seat, attached to hundreds of yellow, red, green and white party balloons.
The priest was flying towards the city of Dourados, some 750 kilometers (465 miles) northwest of his parish, but strong winds forced him off course and his last known location was 50 km (30 miles) off the southern Brazilian coast.
Rescue helicopters and fishing boats are involved in the search and rescue operation to try and locate the priest in the state of Santa Catarina, where pieces of balloons were found floating in the ocean.