"There is no place in the army for people who think this way," Defence Minister Martin Bartak said in a statement following a newspaper report that highlighted the case.
The DNES daily said on Monday that 1st Lieutenant Jan Cermak, a troop commander from the provincial reconstruction team in Logar province, had adorned his helmet with the SS Hohenstaufen division's emblem - the letter "H" crossed by a sword.
Another man, a warrant officer, wore a helmet with the emblem of the SS Dirlewanger division consisting mostly of criminals famous for looting and raping and killing civilians, said DNES, the top-selling Czech non-tabloid daily.
Cermak said he used the emblem because the letter "H" was his initial, pointing at the familiar version of his name - "Honza." "I put it there just for kicks," he said, blaming "youthful recklessness."
Quoting a letter from other soldiers who were upset by the scandal, DNES said Colonel Petr Prochazka, the commander of the contingent, knew about the emblems and covered up as Cermak was his protege.
Bartak, who had awarded medals to the officers concerned only last Friday, said he wanted an "immediate and thorough investigation of the case" as what the soldiers did was "unacceptable and cannot be tolerated."
The scandal, particularly sensitive in the former communist country where far-right extremism is on the rise, leaked a week after the same daily wrote that an elite soldier had trained neo-Nazis for terror attacks and infighting.
Czech troops in Afghanistan also came under scrutiny earlier this year as the Special Operations Unit (SOG) was accused of letting its British command down by refusing to fight terrorists several times "because it's dangerous."
The Czech army, which has lost three soldiers in Afghanistan since 2007, has 330 soldiers and 10 civilians working in the Logar provincial reconstruction team as part of NATO's International Security Assistance Force (ISAF), according to the Defence Ministry website.