Defense Minister Martin Bartak said it was "unacceptable" that two soldiers had reportedly worn symbols of World War II Nazi SS divisions on their helmets while serving in Logar province, in central Afghanistan.
In an interview with the Mlada Fronta Dnes daily, one of the men in question said his behavior was silly and caused by stress. He was shown in a photo wearing a helmet painted with the letter H and a sword on it, an emblem of the Hohenstaufen SS division.
Their commander was suspended for allegedly knowing about the incident but failing to report it.
According to newspaper reports, the scandal was discovered by a diplomat who complained about it back in Prague.
Czech Republic has a 480-strong unit that serves with the NATO-led force in Afghanistan.
"I am sorry this casts a shadow over the entire unit which otherwise is doing a great job," Bartak said.
In a separate case, another professional Czech soldier was fired from the army Monday for belonging to a right-wing extremist group, said Andrej Cirtek, a defense ministry spokesman.