The Daily Times reported the commission also urged authorities to provide protection for the family of the arrested girl, Rimsha Masih, as well as Christians who have fled from the Islamabad area where Masih was arrested Aug. 16 after being accused of burning pages of the Koran.
Earlier media reports had said Local people had beaten up the girl. The issue has raised international concern about Pakistan's anti-blasphemy law, which provides for the death sentence in some cases for criticizing Islam or the Prophet Mohammed, or desecrating the Koran.
Masih, who had lived in a slum area, is in jail, with police quoted as saying it is for her own protection. Her age has variously been given from 11 and up.
There have been conflicting reports about her mental state, with some saying she has Down syndrome.
The New York Times has reported that while it was not known how Masih came into possession of the religious text, one neighbor told the Times it might have been accidentally swept up during trash collection.
The Pakistani rights commission said some reports have said the burned Koranic pages were found in a shopping bag Masih was carrying for disposal when someone stopped her demanding to see what she was carrying, the Daily Times reported. Some clerics were alerted and a mob assembled outside the girl's house, the report said.
The commission said the blasphemy charge against a minor girl who is unwell were beyond comprehension, the Daily Times reported. The commission said blasphemy laws in Pakistan have been misused against religious minorities and unfounded allegations have led to violent attacks against them.
The News International newspaper quoted the commission as urging the government to take steps to ensure the security of all religious minorities, especially Christians, and take stern action against those instigating violence against non-Muslim citizens. Pakistan is a Sunni Muslim majority country.
Hundreds of Christians in the village where Masih lived have left their homes, fearing a backlash, Pakistan's Express Tribune reported, although some have since returned. One police official was quoted as saying some left on his advice.
Amnesty International, citing Masih's case, has asked the Pakistani government to reform its blasphemy law and ensure the girl's safety.
"This case illustrates the erosion of the rule of law and the dangers faced by those accused of blasphemy in Pakistan," said Polly Truscott, the rights group's South Asia director.
Truscott said AI is "extremely concerned" about the girl's safety as in the recent past "individuals accused of blasphemy have been killed by members of the public."
AI said as many as 300 Christian residents in the area had fled, while the girl's family remained in hiding.
Pakistani President Asif Ali Zardari has ordered an investigation into the case and called on the authorities to "protect the life and property of everyone."
While welcoming Zardari's orders, Truscott said they will count for little unless "followed by greater efforts to reform the blasphemy laws to ensure they cannot be used maliciously to settle disputes or enable private citizens to take matters into their own hands."
U.S. State Department spokeswoman Victoria Nuland has said Masih's case "is obviously deeply disturbing" and urged Pakistani authorities to hold an investigation into it in a transparent way.
"And we urge the government of Pakistan to protect not just its religious minority citizens, but also women and girls," Nuland said.
Minorities in Sunni Muslim-majority Pakistan, including Shiite Muslims, have long complained of persecution. At least 22 Shiite bus passengers were gunned down this month after being taken out of the vehicles by gunmen.
The Hindu community, another minority in Pakistan, has said its members are being forced to convert to Islam, and many families are reported to have returned to neighboring India.