Antonino Calixto, mayor of Manila's Pasay district where the American pop phenomenon is due to perform on May 21 and 22, said inspectors will be on hand at the venue to ensure she does not overstep the mark.
"We reminded the producers of Lady Gaga's concert that the show and the event as a whole shall not exhibit any nudity or lewd conduct which may be offensive to morals and good customs," he said in a statement.
"Although we respect artistic and musical expressions, I won't allow anyone or any group to provide acts which may be questionable in (any) way."
Lady Gaga has already faced opposition elsewhere on the Asia leg of her tour, including in Indonesia where police denied her show a permit amid threats from hardliners.
Calixto said religious groups in the Catholic-majority Philippines have expressed concern over the show and that City hall was Friday picketed by several dozen members of a Bible study group offended by Lady Gaga's "Judas".
The group claimed the song "mocks and blasphemes the name and person of the Lord Jesus Christ, who is the central figure of each faithful Christian in the country", Calixto said.
Ovation Productions, the promoters of the Manila concert, told AFP its president Renen de Guia was unavailable for comment Friday.
On Wednesday Lady Gaga's Indonesian promoters vowed to fight to save her show, despite police denying it a permit and hardliners threatening "chaos" if she came to the mostly Muslim nation.
Production company Big Daddy said it still hoped to find a way to hold the June 3 event after already selling more than 50,000 tickets to a concert in Jakarta.
The Islamic Defenders Front (FPI) said it would create havoc if Lady Gaga were allowed to perform in Indonesia, calling her the "devil's messenger" and warning they were ready to die to stop the concert.
In March the Korean Association of Church Communication vowed to take action to stop young people from being "infected with homosexuality and pornography" during the star's concert in Seoul.
But the star has so far failed to tone down her performances. In Seoul, Hong Kong and Tokyo, she rode on to the stage on a mechanical horse, wearing a black bodysuit and an enormous black metal headpiece.
After Manila, the tour heads to Bangkok and Singapore. She was due to play in Jakarta after that, before flying south to New Zealand and Australia.
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Thanks for banning her! She's a devil worshipper! We don't want to listen to her evil lyrics!
Well it's good that she is banned.