21 June 2011 Last updated at 12:29 GMT
Pakistan has banned a number of groups in recent years for supporting militancy and encouraging extremism.
Brig Ali, who is based at military headquarters, was held last month and his family told he would be home soon.
"Yes, that's correct that he is under detention and an investigation is in progress for his contacts with a proscribed organisation," Maj Gen Athar Abbas told BBC Urdu's Asif Farooqi.
He did not provide any more details about the nature of the alleged contact or the organisation the brigadier is accused of being in touch with.
"Any more details at this point in time may affect our investigation process," Gen Abbas said.
'Brilliant' record A senior military officer, who wished to remain unnamed, told our correspondent that senior officers were both surprised and "disturbed" when a secret report was presented to them about the "inappropriate" activities of the brigadier.
The officer is known to have a "brilliant" service record and comes from a family with three generations of military service.
Brig Ali's father was a junior commissioned officer, his younger brother is a colonel serving in the intelligence service. His son and son-in-law are both army captains.
A military source told our correspondent that Gen Ashfaq Pervez Kayani, Pakistan's army chief, had asked for a briefing about the brigadier and after being satisfied about the weight of the "evidence", ordered the arrest himself.
This is not the first time allegations have been made about links between elements in Pakistan's military and banned organisations, including militant groups.
At least two army officers were court martialled last year for links with the banned Hizb ut-Tahrir group.
In 2004 several low-ranking military personnel were convicted in connection with attempts on the life of former President Pervez Musharraf.
Last week, Pakistan's military denied that a major was among several people who had been detained accused of being CIA informants and passing on information which helped the US track down and kill al-Qaeda leader Osama Bin Laden.
A senior officer serving in Pakistan's army has been detained for alleged contacts with a banned militant group.
Pakistan's military spokesman confirmed to the BBC that Brigadier Ali Khan was being interrogated by the country's military intelligence unit.Pakistan has banned a number of groups in recent years for supporting militancy and encouraging extremism.
Brig Ali, who is based at military headquarters, was held last month and his family told he would be home soon.
"Yes, that's correct that he is under detention and an investigation is in progress for his contacts with a proscribed organisation," Maj Gen Athar Abbas told BBC Urdu's Asif Farooqi.
He did not provide any more details about the nature of the alleged contact or the organisation the brigadier is accused of being in touch with.
"Any more details at this point in time may affect our investigation process," Gen Abbas said.
'Brilliant' record A senior military officer, who wished to remain unnamed, told our correspondent that senior officers were both surprised and "disturbed" when a secret report was presented to them about the "inappropriate" activities of the brigadier.
The officer is known to have a "brilliant" service record and comes from a family with three generations of military service.
Brig Ali's father was a junior commissioned officer, his younger brother is a colonel serving in the intelligence service. His son and son-in-law are both army captains.
A military source told our correspondent that Gen Ashfaq Pervez Kayani, Pakistan's army chief, had asked for a briefing about the brigadier and after being satisfied about the weight of the "evidence", ordered the arrest himself.
This is not the first time allegations have been made about links between elements in Pakistan's military and banned organisations, including militant groups.
At least two army officers were court martialled last year for links with the banned Hizb ut-Tahrir group.
In 2004 several low-ranking military personnel were convicted in connection with attempts on the life of former President Pervez Musharraf.
Last week, Pakistan's military denied that a major was among several people who had been detained accused of being CIA informants and passing on information which helped the US track down and kill al-Qaeda leader Osama Bin Laden.
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