According to Centre for Legal Aid, Assistance and Settlement (CLAAS) which works for Christians who are being persecuted because of their faith in Pakistan, a case was registered against the boys on 28th September for "desecrating the Holy Quran or its contents".
The charity said Vishal Masih, a Christian, and Bhola Ram, a Hindu, worked as cleaners for a hospital, and a policeman claims that he received a phone call from a local journalist about the incident.
The police officer was told that the boys burnt government records at Civil Hospital, Dunga, Bhongha, District Bahawalnagar including some pages containing Quranic verses.
Nasir Saeed, Director of CLAAS-UK has accused Pakistan's blasphemy law of increasingly oppressing religious minorities.
He added: "The police register a case against someone without investigation and verbal statements are considered enough evidence to register a case against anyone.
"This incident requires proper investigation into the case before registration, and the policeman is not an eyewitness.
"Since both boys are illiterate, and don't know how to read and write, how can they be charged with committing blasphemy?
"The police needs to investigate those who provided those documents to be burnt.
"It is also important to ask the complainant or eyewitnesses why they didn't stop the burning and what those Quranic verses were."
Saeed has urged the government to ban printed or hand written Quranic verses on office stationary unless it's necessary.