Sharif's orders came after a series of meetings between military and civilian leaders, Dawn newspaper said.
The government delivered a "blunt, orchestrated and unprecedented warning" to the military leadership and sought consensus on several key actions, including action against banned militant groups, the paper quoted unnamed individuals, who were involved in the meetings.
However, asked about the report, Pakistan Foreign Office Spokesman Nafees Zakaria said, "The story you are referring to is purely speculative and as the author himself acknowledged that 'none of the attributed statements were confirmed by the individuals mentioned'."
According to the paper, at least two sets of actions have been agreed as a result of the most recent meeting, an undisclosed one on the day of the All Parties' Conference, which took place on Monday.
ISI Director General Rizwan Akhtar, accompanied by National Security Adviser Nasser Janjua, will travel to all provinces with a message that military-led intelligence agencies should not interfere if law enforcement agencies act against militant groups that are banned.
Sharif directed that fresh attempts be made to conclude the Pathankot investigation and restart the stalled Mumbai attack trial in a Rawalpindi anti-terrorism court.
Separately, on Monday Foreign Secretary Aizaz Chaudhry made a separate presentation in the Prime Minister's Office to a small group of civil and military officials.
The presentation by the Foreign Secretary summarised the results of the recent diplomatic outreach by Pakistan, the crux being that Pakistan faces diplomatic isolation and that the government's talking points have been met with indifference in major world capitals, the paper said.
On the US, Chaudhry said that relations have deteriorated and will likely further deteriorate because of the American demand that action be taken against the Haqqani network.
Chaudhry said while China has reiterated its support for Pakistan, it too has indicated a preference for a change in course by Pakistan.
Specifically, while Chinese authorities have conveyed their willingness to keep putting on technical hold a UN ban on JeM leader Masood Azhar, they have questioned the logic of doing so repeatedly, the report said.
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