Prime Minister Nawaz Sharif has bluntly asked the military leadership, including the ISI, to act against militant groups.
Pakistan's influential Dawn newspaper, citing unnamed sources, said the civilian government, in a "blunt, orchestrated and unprecedented warning", asked military-led intelligence agencies "not to interfere if law enforcement acts against militant groups that are banned or until now considered off-limits for civilian action".
"Prime Minister Nawaz Sharif has directed that fresh attempts be made to conclude the Pathankot investigation and restart the stalled Mumbai attacks-related trials in a Rawalpindi anti-terrorism court," the newspaper said.
It said that the government has informed the military leadership of "a growing international isolation of Pakistan and sought consensus on several key actions by the state".
The government asked spy agency Inter-Service Intelligence (ISI) chief Gen. Rizwan Akhtar and National Security Adviser Nasser Janjua to travel to each of the four Pakistani provinces with a message for ISI's sector commanders.
The decisions were taken after an extraordinary verbal confrontation between Punjab Chief Minister Shahbaz Sharif and the spy agency chief, the newspaper said.
It said that the account was based on conversations with Dawn of individuals present in crucial meetings Nawaz Sharif held this week.