There have been concerns ahead of the 18 September polls that many of the regional commanders responsible for much of the bloodshed in Afghanistan over the past 25 years may try to win seats in the legislature without first disarming and demobilising their militias.
Grant Kippen, chairman of the Electoral Complaints Commission, said evidence brought before the body showed the 21 candidates still had ties to militias - forbidden under the country's electoral law.
The move sparked an immediate denial - and a threat - from one of the candidates, Qumandan Didar, an independent candidate in Kabul.
"My supporters will protest and will sabotage the election process," he said. "I have no weapons. I have completely disarmed and have no links to armed groups. But I still have thousands of supporters."
Didar was a militia commander during the civil war in the early 1990s, but is believed to have fled to neighbouring Pakistan when the Taliban took control of much of the country in the second half of the decade.
The electoral commission released the names of the 21 candidates. None are known to have close ties to President Hamid Karzai.
Some international observers have criticised the process used to disqualify candidates.
The commission relied on evidence provided by a government-backed disarmament agency, raising fears that those in power may exploit the agency to have their rivals removed from the election race.
Kippen said another seven candidates have been disqualified for holding official government posts, which is also barred under the electoral law.
Monday's announcement comes two months after an initial group of 17 candidates was struck from the ballot, including 11 regional commanders.
Nearly 2800 people are running for parliament, while some 3000 others are competing for 34 provincial assemblies.
Meanwhile, Aljazeera correspondent in Qandahar reported that 10 Afghan policemen were killed when a landmine blew up the vehicle they were travelling in, near the border region of Spin Boldak.
No one has claimed responsibility for the attack.