The 26-year-old singer had to drop the scheduled performance following threats from Islamic hard-liners who objected to Gaga's stage acts and costumes saying she would disturb the country's moral fibre.
"We had to cancel the concert in Indonesia. I'm so very sorry to the fans and just as devastated as you if not more. You are everything to me. I will try to put together something special for you. My love for Indonesia has only grown and all its people," Gaga posted on Twitter.
The Islamic hard-liners said that Gaga brings bad influence to the world's most populous Muslim country with her sexy clothes, provocative dance moves and music that promotes homosexuality.
The police, who had denied permission at first, later requested for Gaga to tone down the performance but her manager said that they will perform "the way it is".
As many as 50,000 tickets to the concert were sold out. Organizers could not find another venue to accommodate such large audience anywhere in Indonesia.
"This is a huge concert so it can't be moved elsewhere. Nowhere else in Indonesia can accommodate that many people," concert promoters Big Daddy president director Michael Rusli said, adding it is "unfortunate" that the June 3 concert has to be cancelled in the end.