Pedro Tango, a regional police head, said that Alpariz was found with "two 60 millimetre mortar shells rigged to improvised explosives devices, and two howitzer shells ready to be attached to similar bombs".
"These bombs, if exploded, would cause extensive damage," he said.
Alpariz was said to have been under surveillance for months before he was arrested.
"Although there was no passport recovered from him, he is a known Pakistani national," said Joel Limson, a local police official.
It was not clear how police believe Alpariz was linked with JI.
Police say they suspect two other JI members, Dulmatin and Umar Patek, Indonesian nationals said to specialise in bomb-making, have been hiding in the southern Philippines for months.