Pakistan's army warned Wednesday of "grievous consequences" for the country over criticism by the prime minister that has escalated tensions between the powerful military and the government.

Prime Minister Yousuf Raza Gilani immediately sacked the top bureaucrat in the defence ministry over the row, with the government saying the official had been the cause of the "misunderstanding" with the military.

Tensions between the army and the weak civilian administration have been rising over a memo allegedly written by one of President Asif Ali Zardari's aides that asked for US intervention to stave off a feared military coup in May last year.

The latest clash centres on a Supreme Court inquiry set up to investigate the controversial unsigned memo.

Gilani earlier this week accused the army and intelligence chiefs of failing to make their submissions to the commission through government channels, in an unusually bold interview with Chinese media.

The army Wednesday vociferously denied Gilani's accusation and said it had passed its response through the defence ministry to the court in accordance with the law.

"There can be no allegation more serious than what the honourable prime minister has levelled against COAS (army chief General Ashfaq Kayani) and DG ISI (spy chief Lieutenant General Ahmad Shuja Pasha) and has unfortunately charged the officers for violation of the constitution of the country," the army said in a statement.

"This has very serious ramifications with potentially grievous consequences for the country."

Kayani returned on Tuesday from a visit to China.

The military has carried out three coups in nuclear-armed Pakistan and is considered the chief arbiter of power in the country of 174 million, which has been under military dictatorships for about half its history since independence in 1947.

The current civilian administration headed by Zardari has lurched from crisis to crisis since coming to power in 2008 following elections held a month after the assassination of his wife, former prime minister Benazir Bhutto.

Defence secretary Naeem Khalid Lodhi -- considered more loyal to the military than to the civil leadership -- was fired over what the government called a "misunderstanding" between Gilani and the top brass.

"Prime minister has terminated the contract of defence secretary Naeem Khalid Lodhi for gross misconduct," a senior government official told AFP, though it was not clear what that misconduct was.

The prime minister appeared on national television to launch a new sports channel as the row unfolded, but later sought to minimise the fallout.

"We have nothing against anybody," he told reporters, adding that the army chief had spoken to him before issuing the statement.

"The defence secretary was removed after conducting an enquiry against him. He did not follow the rules of business," he said.

Senior army officers were planning to hold an emergency meeting on Thursday.

The "Memogate" scandal was allegedly an attempt by President Zardari, through close aide Husain Haqqani, then-ambassador to the United States, to enlist help from the US military to head off a feared coup in Pakistan.

American businessman Mansoor Ijaz has claimed that Zardari reportedly feared that the military might seize power in a bid to limit the hugely damaging fallout after US Navy SEALs killed Osama bin Laden in Pakistan in May.

Tensions between the army and Zardari's weak civilian administration soared over the note, allegedly delivered to then chairman of the US Joint Chiefs of Staff Admiral Mike Mullen in May and made public by Ijaz in October.

Pakistan's Supreme Court last week decided to set up a judicial commission to investigate the matter and Pasha, the head of the ISI intelligence agency, has called for a "forensic examination" of the memo.

The government is expected to set out its case to the court on January 16.

The commission is due to complete its probe by the end of the month, putting fresh pressure on the president, who visited Dubai in December over health fears, with most observers expecting early elections sometime in 2012.