The military yesterday confirmed that Brig Ali Khan, serving as director for rules and regulations at the General Headquarters in Rawalpindi, had been detained.
Reports said Khan was suspected of having links with Hizb-ut-Tehrir, a group that has been calling for a rebellion against "pro-America" leaders.
Khan, who had trained in the US and was set to retire soon, was denied promotion in the past because of his extremist leanings, the Dawn newspaper reported on Wednesday.
Before his posting at General Headquarters, Khan served as a commander in Pakistan-occupied Kashmir.
Before his arrest, Khan was under surveillance because of his contacts with extremists and he was held for interrogation once those interactions became too frequent, sources told the newspaper.
Khan`s detention was approved by army chief Gen Ashfaq Parvez Kayani who was "very disturbed" to learn about the infiltration of Hizb-ut-Tehrir at such a senior level, a source said.
Khan was detained by the military`s Special Investigation Branch on May 6, four days after al-Qaeda chief Osama bin Laden was killed in a covert US raid in the garrison city of Abbottabad. He is the senior-most military officer to be arrested for extremist links.
A defence source told the Dawn that a lieutenant colonel who worked under Khan had also been detained but another official said the arrest was not directly linked to Khan`s case.
The confirmation of Khan`s detention came at a time when some elements in the military are being accused of being in collusion with extremists and militants.
Senior journalist Syed Saleem Shahzad was abducted and killed two after he alleged in an article on May 27 that al-Qaeda had infiltrated the Pakistan Navy. Reports have suggested that a terrorist raid on the PNS Mehran naval airbase in Karachi on May 22 had support from within the navy.
Inter-Services Public Relations chief Maj Gen Athar Abbas played down Khan`s links with extremists as "an exception".
He told Dawn that though there was zero tolerance in garrisons for religious and sectarian organisations, the "ranks could not remain unaffected by what was happening in the society -- a reference to rising extremism in the country".
Khan, the son of a retired junior commissioned officer, has a strong military background.
His brother is serving in a military intelligence agency and his son and son-in-law are captains in the army.
The Hizb-ut-Tehrir, which started operating in Pakistan in the late 1990s, has been striving to infiltrate military ranks. It first enlisted some Pakistan Army officers while they were training at Sandhurst in Britain in 2000.
These links were exposed in 2003 when some officers were arrested, prompting then military ruler Pervez Musharraf to ban the organisation.
The US reportedly alerted the Pakistan Army in 2009 about the penetration of Hizb-ut-Tehrir into its ranks and the presence of the group`s cells in the military.