Zakaria Kandahari was picked up "recently" in the southern city of Kandahar for "various crimes," in a special operation conducted by the Afghan National Directorate for Security, the intelligence agency said in a statement.
It did not elaborate, but the Defence Ministry has said Kandahari was wanted on charges of murder and torture in connection with the disappearances of nine boys and men who turned up dead.
The US-led coalition has denied any involvement in the disappearances, but the case has further strained Washington's relations with President Hamid Karzai, and could complicate plans to leave special operations forces in Afghanistan after combat troops complete their withdrawal next year.
When the allegations about Kandahari surfaced, Karzai ordered US special forces out of the Narkh district of Wardak province, where the disappearances occurred. Karzai had originally ordered them out of the whole province but General Joseph Dunford, the top US commander in Afghanistan, said such a move would threaten the security of Kabul, 45 kilometres south.
When he was arrested, Kandahari had three pistols, two fake Afghan National ID cards and seven other false IDs on him, the intelligence service said.