Abdulahi Hassan Afrah said Saturday two of the men had both a hand and a foot cut off and a third had only a foot cut off after the Islamic court in the southern port city of Kismayo realized he was already disabled.
He says the three screamed as six masked men carried out Friday's judgment using machetes.
A spokesman for the al-Shabab militia, Sheik Hassan Yaqub Ali, says they admitted robbing a truck.
They weren't allowed to appeal or have access to lawyers.
The Islamic courts were originally set up to try to counter the bloody chaos of the civil war. They formed the basis of the insurgency currently fighting the government.