Pakistan Prime Minister Yousuf Raza Gilani sacked his defence secretary on Wednesday for "gross misconduct" as tensions with the military exploded following an army warning to the civilian leader.
"Prime minister has terminated the contract of defence secretary Naeem Khalid Lodhi for gross misconduct," he said.
State media said he had been fired "for creating misunderstanding between the state institutions".
The army earlier said the defence ministry had failed to process its submissions made to a Supreme Court inquiry into a controversial unsigned memo that sought US help in curbing the power of the military.
The move by Pakistan's prime minister came as fears grow the country's powerful military is bent on ousting the government.
The channels did not give a reason why the secretary, Retired Lieutenant General Khalid Lodhi, who was the top defence bureaucrat, was fired.
The move comes amid high tension over an unsigned memo that sought U.S. help in reining in Pakistan's generals.
Pakistan's military is warning of 'grievous consequences' after the prime minister was reported to have accused the army chief and the head of the spy agency of violating the constitution.
The military statement Wednesday is the latest sign of a destabilising clash between the army and the government of President Asif Ali Zardari, which many commentators believe could end in the dismissal of the current administration.
Prime Minister Yousuf Reza Gilani was quoted as telling a Chinese newspaper that army chief Gen Pervez Ashfaq Kayani had violated the constitution by submitting statements to the Supreme Court about a scandal involving a memo sent to Washington that is rocking the country.
The army statement said this had "very serious ramifications with potentially grievous consequences for the country."
It did not elaborate.
Distrust between civilian leaders and the generals has bedeviled the nuclear-armed South Asian country for almost its entire existence, with the military ruling for more than half of its 64-year history after a series of coups.
A senior military official said the latest tension was "very serious".
In December, President Zardari flew to Dubai for medical treatment sparking rumours that he had fled the country anticipating a coup.
Gen Kayani last month dismissed coup rumors as speculation and said the army supported democracy. Zardari returned after about two weeks.