Police in Indonesia had refused to issue a permit for Lady Gaga after Islamic groups objected to her show, claiming it was too vulgar.
The hard-line Islamic Defenders Front (FPI) had threatened to try to stop Lady Gaga getting off the plane.
Indonesia is officially secular but has more Muslims than any other country.
More than 50,000 tickets had been sold for the 3 June event. Promoters said they would offer refunds.
“Lady Gaga’s management has considered the situation minute to minute, and with threats if the concert goes ahead, Lady Gaga’s side is calling off the concert,” Minola Sebayang, lawyer for promoters Big Daddy, told reporters.
This is not the first time that Lady Gaga has faced objections during her Asian tour.
Her concert in South Korea in April was made an adults-only event following protests from Christian groups.
Protests also took place in the Philippines, with Christian groups accusing her of being blasphemous.
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