Protesters calling for Prime Minister Nawaz Sharif to step down also briefly forced their way into the office of Pakistan TV. The Army had to step in to secure the state-run broadcaster's premises.
After a brief calm due to overnight rain, the protesters armed with clubs and sticks this morning broke the gate and entered the premises of the secretariat, defying calls from the army personnel not to enter inside the building.
Police fired rubber bullets and tear gas shells to push them back but remained unsuccessful. The protesters damaged vehicles of employees of the secretariat.
The fresh clashes came hours after an emergency meeting of army corps commanders last night who expressed serious concern over the prevailing political turmoil in the country with the government of embattled Prime Minister Nawaz Sharif locked in a showdown with Pakistan Tehreek-i-Insaf chairman Imran Khan and Pakistan Awami Tehreek chief Tahir-ul Qadiri.
The generals, who have ruled Pakistan for more than half of its history since independence from Britain in 1947, said that the "situation should be resolved politically without wasting any time and without recourse to violent means".
The last 48 hours saw the anti-government protests morph the high-security Red Zone from a concert ground to a bloody battlefield, with three people killed and over 550 injured.
Thousands of supporters of Khan and Qadri are battling with the police since Saturday night to reach in front of the PM House, the official residence of Prime Minister Sharif.
The clashes started when both Khan and Qadri asked their followers, camping in front of the parliament house, to shift the venue of protest to lawns of PM House on Saturday night.
The protesters fought pitch battles with the police until the heavily shower forced them to halt pelting stones at them last night. After the rain stopped, the protesters this morning resumed clashes.
Dozens of policemen have been injured in the clashes.
The News reported that a case has been registered against Khan for inciting violence and encouraging attack at the security forces and the parliament, a charge denied by him.
Khan and Qadri have snapped communications with the official negotiators after the fifth round of talks failed to produce any result last week.
Khan wants the PML-N government's ouster over alleged rigging in last year's poll which his party lost, while Qadri wants to bring a revolution in the country. Both the leaders are agitating since August 14.