Karzai was re-elected as president after widespread voter fraud was revealed, depriving him of the 50 per cent win he needed to avoid a run-off. His main rival pulled out of the second round and Karzai was re-appointed.
Atmar added: "The idea of the unit is that all top-level employees in Afghanistan involved in corruption should be held responsible, both civilian and military and, if proved guilty, they should be fired and prosecuted in accordance with the law."
Although Atmar said the new measures were not the result of international pressure "but for the sake of the Afghan people", his announcement comes after widespread criticism and demands from Washington for the government to do more about fighting corruption.
"The idea of the unit is that all top-level employees in Afghanistan involved in corruption should be held responsible, both civilian and military and, if proved guilty, they should be fired and prosecuted in accordance with the law"
Mohammad Hanif Atmar, interior minister
Gordon Brown, the British prime minister, also recently warned Karzai that the West would withdraw its support if he failed to tackle corruption.
Karzai is due to be inaugurated on Thursday for his second term.
Atmar was flanked by Karl Eikenberry, the US ambassador to Afghanistan, and his British counterpart, Mark Sedwill, as he made the announcement.
On Sunday, Hillary Clinton, the US secretary of state, had warned that Karzai and his government must do better and that Washington and Afghanistan's other allies wanted to see tangible evidence of the fight against rampant corruption.
The new anti-corruption unit, formed as part of the attorney-general's department, will have prosecutors trained by officials from the EU police mission in Afghanistan, as well as others from Britain and the US, according to the interior ministry's statement.
Training and vetting for the new prosecutors would include polygraph tests.
Afghan leaders, including Karzai and Hazrat Omar Zakhilwal, the finance minister, have railed at heavy criticism from the West since Karzai's re-election was confirmed earlier this month despite widespread vote fraud and questions being raised about the independence of Afghanistan's Independent Election Commission.
Zakhilwal told the Reuters news agency in an interview at the weekend that Western countries must share the blame for corruption in Afghanistan.
Without naming names, he said politicians in the West were using the issue to make domestic political mileage.