Mir, 50, a popular news anchor, terrorism expert and security analyst on Geo TV, had survived an attempt on his life in 2014 when gunmen shot him thrice.
The seasoned journalist faces threats from multiple quarters including the Taliban.
Khalid Khawaja of the powerful spy agency Inter-Services Intelligence (ISI) was kidnapped along with former army Colonel (retd) Imam, British journalist Asad Qureshi and driver Rustam Khan by militants in the restive South Waziristan in 2010.
Family of Khawaja, who was a retired officer of Pakistan Air Force, accused Mir of kidnapping him.
More From This Section
Islamabad High Court Judge Mohsin Akhtar Kayani ordered the registration of a case last week following a petition by Khawaja's widow Shamaima Malik.
The case was registered yesterday at the Ramana police station against Mir who has not been arrested.
Murder clause has not been included in the case and Mir faces only allegations of kidnapping. If convicted, Mir faces a seven-year jail-term.
Meanwhile in his defence, Mir said that he had already been declared innocent in the case, but now he was being victimised for standing up to the cause of a free media.
Currently, Mir is leading a team investigating an attack by unknown people on local journalist Mutiullah Jan.
He is also part of a group investigating registration of a case against another journalist Arshad Sharif.
Mir survived an attempt on his life in 2014 when gunmen attacked his car in Karachi. He was admitted to a hospital in serious condition but survived.
Both Mir and Noorani work for the largest Jang/Geo media group, which owns Geo TV and Jang newspaper in Urdu.