Nnamdi Kanu has not been seen in public since troops were deployed to Umuahia, Abia State last month.
Kanu, who wants a separate state for the Igbo people who dominated the country’s southeast, has been on bail since April.
He is scheduled to appear in court in Abuja on Tuesday.
His lawyer, Ifeanyi Ejiofor, told AFP: “Only the army can tell us where he is. Either they arrested him or they killed him.
“If he is alive, they should bring him to the court on Tuesday.”
Justice ministry spokesman Salihu Othman Isah said whether the trial goes ahead depends on Kanu’s appearance and the judge.
“I can’t tell you specifically what will happen,” he added.
Kanu’s disappearance has prompted renewed fears of violence in the restive southeast, which remains tense 50 years after a declaration of independence sparked a brutal civil war.
He was first arrested in October 2015 and held in custody until April this year, despite repeated court rulings that he should be released.
In Umuahia, which was once the capital of the self-styled republic of Biafra and where Kanu spent his childhood, the windows of the family home have been blown out.
The ochre walls and the cars parked in front of the building are pitted with bullet holes, according to an AFP correspondent in the city.
Kanu’s younger brother, Prince Emmanuel Kanu, maintains he was at the compound when soldiers attacked it on September 14.
He said 28 people were killed but the army has denied the claim. Neither claim has been verified independently.
“They were so numerous. They started to shoot from 200 metres (650 feet) away,” Prince Emmanuel told AFP by telephone. “People were running for their lives. We had no guns with us.”
Prince Emmanuel said the military was holding his brother in secret. The government has dismissed the claim and said he was “hiding” somewhere.