Pakistani Taliban chief Hakimullah Mehsud has issued "special directions" to his subordinates in different cities of Pakistan to target media groups, BBC Urdu reported.
An unnamed Interior Ministry official said intelligence agencies had intercepted a phone conversation between Mehsud and a subordinate named Nadeem Abbas alias Intiqami, in which the Taliban chief was heard directing Abbas to attack media organisations.
Mehsud directed Abbas to target offices of media groups in Karachi, Lahore, Rawalpindi, Islamabad and other cities.
Media groups and personalities who were denouncing the Taliban after the attack on Malala should be the focus of such attacks.
The Interior Ministry has issued orders to beef up security near the offices of media organisations in Pakistan following Mehsud's call, the official told BBC Urdu.
Authorities have been directed to deploy additional policemen in areas where media offices are located.
The help of the Frontier Constabulary will be sought if needed, the official said.
The Chief Commissioner of Islamabad and Chief Secretaries of the four provinces have been directed to meet owners of media groups and address their security concerns.
The ministry has also alerted religious scholars who had publicly denounced the Taliban to be cautious, the official said.
The National Peace Award winner is currently on ventilator in the critical care unit of a military hospital in Rawalpindi after doctors removed a bullet lodged near her spine.
Malala and two schoolmates were injured when Taliban fighters opened fire on their school van in Mingora, the main city of Swat.
The Tehrik-e-Taliban Pakistan claimed the responsibility for the attack, saying Malala was targeted for backing pro-West views and a secular government.
A Taliban spokesman has also threatened to kill Malala's father Ziauddin Yousufzai and other members of her family.