The dismissed charges bordered on “ownership of unlawful society, illegal importation of radio transmitters and researching on how to make improvised explosive devices”.
A magistrate court in Abuja had thrown out similar charges in 2015.
Nyako said she took the decision to quash the six charges because the prosecutor did not present any evidence.
However, she held that Kanu would be re-arraigned on a five count of treasonable felony.
On January 12, Ifeanyi Ejiofor, Kanu’s lawyer, had prayed the court to quash the charges against his client because he had not committed any offence by agitating for Biafra.
On Tuesday, Chukwuma Soludo, former governor of the Central Bank of Nigeria (CBN); Patrick Utomi, a professor of economics, and some Igbo leaders called for the immediate release of Kanu.
They described his trial as persecution, and they asked the government to release him for the sake of engineering a new Nigeria.