Temur Shah was detained on Tuesday in a joint operation by police and intelligence agents, outgoing Interior Minister Ali Ahmad Jalali said at a news conference on Wednesday.
Jalali said Shah is accused of kidnapping Clementina Cantoni, abducting and killing the son of an Afghan businessman and threatening a bank chairman in an extortion attempt a few days ago.
Shah had been detained earlier but released for unspecified reasons, the minister added.
Cantoni reportedly identified Shah in photographs shown to her by investigators.
Cantoni, who had been working for CARE International in Kabul, was abducted by armed men on 16 May and released in the Afghan capital on 9 June.
Italian newspapers reported that her freedom was secured thanks to the release of Shah's mother, one of four people who had been detained for alleged links with the kidnappers.
But Interior Ministry officials said the release of the mother and the other three was not part of a deal with Cantoni's kidnappers.
Cantoni, 32, said she was treated well while in captivity and was moved once by her captors.
Italian newspapers quoted her as saying the only person she had spoken to as a captive was Shah, whom she said told her his name shortly after she was abducted.
Cantoni had been working on a project helping Afghan widows and their families.
Private Tolo television showed footage of Shah along with another man and a woman. All three were detained in Kabul late on Tuesday.