The source said the defendants, two people who carried out the circumcisions and four parents, were accused of mutilating seven young girls. No further details were available.
The government-run National Committee for the Abandonment of Harmful Practices, which brought the complaint, said it hoped the group would get long sentences, although they have yet to be convicted.
The committee’s spokesman Fatima Djau Balde said he hoped the prosecutions would “be a lesson to those still thinking of perpetuating this harmful and retrograde practice”.
Female genital mutilation is usually carried out on girls between infancy and age 15. It can cause infections and, later, infertility and childbirth complications.
According to a health ministry report released in 2012, at least 320,000 women and young girls have undergone FGM in the nation of 1.7 million.
It said the practice was most widespread among Muslim communities such as the Mandinka and Fula.
The Bissau-Guinean parliament passed a law in June 2011 banning FGM and making it a crime punishable by up to five years imprisonment.
The maximum penalty is five years in prison and a fine of 50 000 CFA francs ($95, 76 euros).
Aid agency Plan International said earlier this year 50 percent of girls continue to be victims.