A resident of Beledweyne in central Somalia who identified himself only as Ali told The Daily Telegraph the girls were shot in the back as they sat with their arms pinioned behind them in the central square.
"The group informed the population that a punishment was going to be carried out in public on two women they claimed had been found guilty of spying," Ali said. "I didn't know they were planning to shoot them.
"It was shocking. They looked so young. They looked so desperate, but no one could help."
Sheik Yusuf Ali Ugas, the al-Shabaab commander in the town, issued a statement calling the girls "evil" and saying they had admitted espionage, CNN reported.
"My cousin, Ayan Mohamed Jama, was just 16 years old and she was absolutely innocent," a relative told CNN.
He said the other girl was 15 and that the militants did not allow their families to talk to the girls before they were executed.