Fauzia, a 13-year-old girl and one of those affected in the latest incident, said when she stepped out of the classroom she "smelled a strange odour and then fainted".
"I don't think my parents will allow me to attend the school after
this incident," she said.
Another girl, 12-year-old Sumaila, said she was in class "when a smell like a flower reached my nose".
"I saw my classmates and my teacher collapse and when I opened my eyes I was in hospital"
"I saw my classmates and my teacher collapse and when I opened my eyes I was in hospital."
Humayun Khamoosh, head of the Central Hospital in Kunduz, said all the girls were in stable condition after initial treatment.
Authorities said they were still investigating the incidents.
Waheed Omer, a spokesman for Hamid Karzai, the Afghan president, said anti-government groups intent on spreading fear were to blame for the incidents.
"Whoever prevents children from going to school is an enemy of Afghanistan and its prosperity," he said.
Taliban denies involvement
But a Taliban spokesman denied the group had any involvement in the attack, and condemned the targeting of school girls.
Girls' schools have been attacked in similar fashion in other parts of Afghanistan over the past few years.
In one attack in Kandahar in 2008, around 15 girls and teachers were sprayed with acid by men on motorbikes.
During Taliban rule, from 1996-2001, girls were banned from attending school.
In parts of southern and eastern Afghanistan, particularly in Taliban strongholds, schools for girls still remain closed.