Concerned at the unwarranted checks, they said the practice amounts to trampling on human rights and respect for their privacy.
Several individuals from different parts of the capital said that armed men had informed them that their smartphones would be checked, the report said.
A senior government official, however, said the security forces did not have the right to peep into people's mobile phones or harass citizens.
But in some cases, the official believed, intelligence agents might have done so on the basis of tip-offs. He promised an end to the practice.
Bilal Karimi, deputy spokesman for the caretaker government, also acknowledged that the security forces did not have the right to examine mobile phones or harass citizens, the report said.
In some instances, intelligence operatives could have searched the phones of certain suspects on the basis of a tip-off. However, he said, this had not happened to all the citizens.
He added: "Mujahideen of the Islamic Emirate is not doing this; but the name of the Mujahideen may have been misused, and those who face such problems should inform the authorities."
He claimed that many men, who were harassing the people, have been arrested and efforts are being made to crackdown on such imposters.