Guinea-Bissau's highest court has ordered the release of a former armed forces chief detained for more than three months over suspected involvement in a failed 2012 coup attempt.

Jose Zamora Induta, a rear-admiral who was ousted as military chief of staff in 2010, was placed under house arrest after returning from exile in Portugal in July and transferred to an army barracks in September.

The Supreme Court ruled late on Wednesday however that the military tribunal which ordered his arrest had no jurisdiction "because the crime for which Zamora must answer is not a crime of a military nature".

"My client is ready to face justice to clarify the charges hanging over his head, but not before a military court that has no legitimacy to judge such cases," his lawyer Jose Paulo Semedo told AFP on Thursday.

Induta remained in Bissau after being forcibly removed by Antonio Indjai but eventually fled to former colonial power Portugal after Indjai led a coup in April 2012.

Induta claimed to have survived an assassination attempt by soldiers linked to Indjai during the mutiny against interim president Raimundo Pereira and his prime minister, Carlos Gomes.

Semedo said Induta had come to Bissau to collect data for a doctoral thesis and, a few days later, was called to testify at the military tribunal over his alleged role in an attempted coup in October 2012 and placed under house arrest.

The October 21, 2012 dawn attack on an elite "Red Beret" army barracks in Bissau left at least seven people dead, including six of the attackers.

Transition authorities in the west African nation have accused Portugal of instigating the attack in a bid to re-instate former prime minister Carlos Gomes Junior, who was ousted in an April 12 coup.

Induta was charged in October of participation in a terrorist organisation, attempting a coup and murder.

Guinea-Bissau has been plagued by coups since independence from Portugal in 1974 and the instability has attracted South American drug cartels using the country as a transit point to Europe.

The country of 1.6 million says it has reintroduced the rule of law since electing Jose Mario Vaz last year in polls that were judged by the European Union as "free and credible".