"We call on the Pakistan Electronic Media Authority not to act on this spurious complaint, and we call on Pakistan's security services to recognise the critical role of the media and exercise tolerance and maturity," said Bob Dietz, Asia programme coordinator of the Committee to Protect Journalist (CPJ).
"The ISI is free to rebut allegations in the media but should not try to censor coverage," Dietz said in his statement.
The media regulator has the authority to shut down broadcasters based on such complaints, and has done so under previous administrations of Pakistan.
Tension between Pakistan's military, intelligence communities and much of the media swiftly escalated following an assassination attempt on Geo TV anchor Hamid Mir, a known critic of the Taliban and the ISI, on April 19, CPJ said.