The balloon, designed by the National Aeronautics and Space Administration (NASA) to detect ultra-high energy cosmic particles from beyond the galaxy as they penetrate the earths atmosphere, is expected to circle the planet two or three times.
"The origin of these particles is a great mystery that wed like to solve. Do they come from massive black holes at the centre of galaxies? Tiny, fast-spinning stars? Or somewhere else?" Angela Olinto, a University of Chicago professor and lead investigator on the project, said in a statement.
The balloons monitoring was only the start of a long quest which would next involve a space mission currently being designed by NASA, she added.
The balloon, launched on Tuesday in Wanaka, a scenic spot on New Zealands South Island, will collect data from 34 km (21.1 miles) above the earth.
New Zealand was also the base for NASAs scientific balloon programme in 2015 and 2016, Reuters reported.