Indonesian police spokesperson Boy Rafli Amar told The AP on Tuesday (May 15) that a permit for the concert was being revoked amid safety concerns.
Hardline religious groups had announced that they would picket the June 3 concert, leading police to determine that they couldn't guarantee the safety for attendees.
The 'Born This Way Ball' show's Indonesian promoter Michael Rusli said he was upset by the ruling, which he blamed on the threats of "troublemakers".
"We are mature enough to be able to separate our own moral values from arts and culture," Rusli told the news agency.
Lady GaGa has not yet commented on the cancellation.
This incident is the latest in a series of protests GaGa has faced since bringing her 'Born This Way Ball' tour to Asia in April.
She is next scheduled to perform in Taipei, Taiwan on Thursday (May 17).
Tickets for Lady GaGa's 'Born This Way Ball' UK tour are now available here.
Watch Lady GaGa perform 'Americano' below: