Mullah Baradar is said to favour talks with the Afghan government
Pakistan has confirmed that a Taliban suspect captured earlier this month is one of the organisation's top leaders, Mullah Abdul Ghani Baradar.
But Interior Minister Rehman Malik denied any US agents had been involved in the operation in Karachi.
Mr Malik also said other suspects had been arrested in the swoop "seven to 10 days ago" and were being interrogated.
The White House described Mullah Baradar's capture as a "big success for our mutual efforts in the region".
Breaking the US silence on the arrest, presidential spokesman Robert Gibbs said on Wednesday the detention was a significant development for joint US-Pakistani efforts to combat Islamist extremists.
The Taliban say Mullah Baradar, thought to be their second-in-command, is still free and is in Afghanistan.
US officials had said on Tuesday that Mullah Baradar was seized by US and Pakistani agents in Karachi on 8 February.
But Mr Malik "categorically" denied US agents had taken part.
"Nothing of the sort has happened. The operation was carried out by Pakistani security agencies."
He said only Pakistani agencies were involved in the interrogation process, but added: "Yes, there is a sharing of intelligence because we are fighting the war together."
Mr Malik described the capture of a man "very close to [Taliban leader] Mullah Omar" as "a big catch for Pakistan".
"It's a serious setback for them. He is a main military commander," he said.
"Others were also arrested and are being interrogated. But it's too early to say anything about them. We will disclose details when the time comes."
The interior minister said the operation showed "how sincere and serious we are on the war on terror".
A separate operation on the Afghan border had led to several further arrests and the seizure of a number of suicide bomb jackets and landmines, he said.
Mullah Baradar is believed to have run the Taliban's leadership council and controlled their finances.
Rehman Malik denied US agents had been involved in the capture
The news of his arrest came as Nato forces and Afghan troops are conducting a major offensive against the Taliban in Afghanistan's southern Helmand province, an area Mullah Baradar is believed to have been responsible for.
His influence within the Taliban is said to be second only to that of Mullah Omar, who has been hiding from Western agencies since the 9/11 terror attacks in 2001.
The arrest suggests Pakistan is getting tough with Afghan Taliban leaders sheltering there, says the BBC's Orla Guerin in Islamabad, something that has long been a demand of the White House.
It could also put pressure on other Taliban leaders to enter into talks with the Afghan government and coalition forces, something Mullah Baradar is believed to favour, our correspondent says.
Afghan and Nato leaders have said reconciliation talks with more moderate Taliban members could be pursued to end the insurgency.
Meanwhile, missiles fired by a suspected US drone aircraft have killed at least three militants in north-west Pakistan, security officials say.
The attack targeted a compound in Tapi Tolkhel village, 15km (9.3 miles) east of Miranshah, the main town in North Waziristan, by the Afghan border.
The regions of North and South Waziristan are known sanctuaries for al-Qaeda and Taliban militants who move easily across the mountainous border into Afghanistan.
They are frequently targeted by drone attacks and there have been more than a dozen such strikes in 2010.