Anas Haqqani, the son of the Taliban-affiliated network's founder Jalaluddin Haqqani, and Hafiz Rashid, a military commander, were picked up in Bahrain and later taken to Afghanistan, the Wall Street Journal reported.
The Taliban said that Haqqani and Rashid were arrested on October 12 in Bahrain by US forces, and taken to Qatar and the United Arab Emirates before reaching Kabul, the paper said.
A senior Afghan security official confirmed the two men were arrested abroad but declined to say in which country.
He said the operation was led by Afghanistan's intelligence service, the National Directorate of Security, and that US forces played no role, the paper said.
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The Haqqanis, while acknowledging the Taliban leadership's authority, operate independently.
"It is unclear what role, if any, authorities in Qatar, Bahrain or the UAE. Played to facilitate the arrests. Officials from the three Gulf states didn't respond to requests for comment," the paper said.
US and Afghan officials have said Pakistan's spy agency ISI covertly backed the Haqqanis to extend its influence in Afghanistan, a charge Islamabad repeatedly deny.
Anas Haqqani, the youngest son of Jalaluddin, rose through the ranks of the group after two of his brothers were killed, and was the second-in-command after his brother Sirajuddin at the time of his arrest, Afghan officials said.
Taliban said that before their arrest the two men had visited Qatar to meet Rashid's brother, Mohammad Nabi Umari.
Last year, the Taliban opened a political office in Qatar to host peace talks with the US and Afghan governments.
The Haqqani network is blamed for a bloody bombing of the Indian embassy in 2008 that left 58 people dead, a 2011 attack on the US embassy, and several big truck bombing attempts.