Gul Bukhari, 52, was detained for several hours by unknown men in the eastern city of Lahore late Tuesday, one day after the military held a press conference warning that it is monitoring citizens who criticise Pakistan.
She was released early Wednesday.
Pakistan has a history of enforced disappearances, often of people who criticise the security establishment -- largely seen as a red line few dare cross. The kidnappings have become increasingly brazen in recent years.
Bukhari is known for advocating human rights online and is also a prominent columnist whose articles are often highly critical of the military and its policies.
When news of her abduction broke it caused a furore, with widespread calls for her release and fingers broadly pointed at the military.
The British High Commission expressed "concern" at the incident as activists called on the army, which is the most powerful institution in Pakistan and has ruled the country for nearly half its 70-year history, to tolerate dissent.
"(The) army is not behind the abduction of Gul Bukhari," Major General Asif Ghafoor, chief military spokesman, told reporters late Friday.
"We actually want a thorough investigation in this case," he said.
The military routinely says it is not involved in enforced disappearances, but the statement was a rare on-the-record denial.
It came as the powerful army is facing growing criticism of its policies within Pakistan, from disappearances to the use of militant proxies in Afghanistan and India.
A burgeoning civil rights movement by the country's ethnic Pashtuns and recent comments from former prime minister Nawaz Sharif have increasingly criticised the generals and caused uproar in the country.
Journalists have spoken of "pressure" not to cover the criticisms, adding to an atmosphere of repression.
During a wide-ranging press conference Monday that appeared to address the mounting criticism, the military issued a veiled warning to online critics, saying it has the capacity to monitor social media accounts.
Ghafoor briefly flashed an image on screen showing what appeared to be Twitter handles and names, including of at least one prominent journalist, but refused to elaborate further, fuelling the outcry over free speech.
Late Friday he said they "did not intend to implicate journalists".
Activists remained sceptical of the military's role in disappearances and curtailing of free speech.
"If they did not do it, then they need to come up with an action, a plan of enquiry (to investigate) who did," said Shahzad Ahmed, head of Bytes for All, a think-tank working for digital security and free speech.
"So far the fingers are being pointed towards them."
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