"The militants shot dead two civilians in Gur Tepa area and another in Chardara district on Friday on charges of spying for Afghan and international troops," Yaqubi told Xinhua.
However, Yaqubi added that the victims were ordinary people and had no links with the government.
Taliban militants who often target government interests have not made comment. A relatively peaceful province until early 2009, Kunduz has been the scene of spiraling militancy over the past several months.
Editor: Zhang Xiang