Javed Ali Khan, a local government official in Mohmand, said that a tribal militia picked up Omar and handed him over to security forces.
Omar's capture would be another blow to the Tehrik-e-Taliban Pakistan after the reported death of Baitullah Mehsud, the group's leader, in a US missile attack on August 5.
'Treasure of information'
Omar frequently contacted journalists to issue statements claiming responsibility for suicide bombings and other attacks across the country.
"The Pakistani government considers Maulvi Mohammed Omar as treasure of information that may lead to many locations of Taliban movement and probably to the fate of Baitullah Mehsud," Al Jazeera's Ahmed Barakat, reporting from Islamabad, said.
"Omar was also Taliban’s deputy emir of Bajaur district. He disappeared around six months ago as he was wanted by the government."
On Monday night, police said they arrested a senior Pakistani Taliban commander and close aide to Mehsud as he was being treated in a private hospital in Islamabad, the capital.
Qari Saifullah apparently told police he had been wounded in a US drone attack in South Waziristan. It was unclear if it was the same raid believed to have killed Mehsud.
There has been much speculation over the fate of Mehsud since the reported US drone raid on his father-in-law's home. The government in Islamabad has said it is "almost certain" that he was killed, but his aides have insisted that he survived the attack.
Richard Holbrooke, the US special envoy to Pakistan and Afghanistan, said during a visit to Pakistan at the weekend that Mehsud was "gone" and it looked as if there was a struggle for succession among his commanders.
The Pakistani military has been targeting Taliban fighters in the South Waziristan in recent months in preparation for what military officials have said will be a major offensive to push them out of the region.
However, Nadeem Ahmed, an army commander, said on Tuesday that the military would need months to prepare for an offensive in South Waziristan due to shortages of "the right kind of equipment" and helicopters being used elsewhere in the country.