The imam's arrest could get the girl, who supporters say is mentally handicapped, out of prison, where she faces up to a life sentence for desecrating the Quran. A bail hearing is scheduled for Monday.
But Christians who fled the neighborhood when the girl was arrested worry about the use of laws that critics say are often abused to settle scores or target minorities.
"We all are suffering," said Somera Ashraf, a Christian woman from the girl's neighborhood.
Ashraf and her family fled the neighborhood with many other Christians when the blasphemy allegations came to light, fearing retribution. She only recently returned but still doesn't feel safe.
Police said Chishti planted pages of a Quran in a shopping bag containing burned papers and ash that had been carried by the Christian girl. The bag was then submitted as evidence to the police.
A member of his mosque came forward Saturday - more than two weeks after the girl's arrest - and accused the imam of planting the evidence, said the investigating officer, Munir Jaffery.
The case has shone an uncomfortable spotlight on the punishments for violating Pakistan's blasphemy laws and caused an uproar in the country, largely because of the girl's age and questions about her mental capacity.
The girl's supporters say she is 11 years old and has Down syndrome; a medical board said she was about 14 and that her mental age didn't match her physical age.
The Associated Press does not generally identify juveniles under 18 who are accused of crimes and is withholding her name.
The girl's lawyer, Tahir Naveed Chaudhry, said the imam's arrest proves his client is innocent and said he will likely move to throw the case out on Monday.
Rarely if ever are people who bring blasphemy charges investigated or arrested for misuse of the law.
Ali Dayan Hasan, head of Human Rights Watch in Pakistan, said the decision to act against the cleric was "unprecedented."
"What it indicates is a genuine attempt at investigation rather than blaming the victim, which is what normally happens in blasphemy cases," said Hasan. "They are actually taking a look at incitement to violence and false allegations. It is a welcome and positive development."