Al-Zawahri has been thought to be in Egyptian police custody for at least three years, but the Egyptian government never acknowledged it until Thursday. He was sentenced to death in absentia for his role in Jihad attacks inside Egypt.
His older brother, Ayman al-Zawahri, is the top aide to al-Qaida leader Usama bin Laden and once led Jihad. In the same military trial, he also was sentenced to death in absentia for Jihad acts.
Egyptian Interior Minister Habib al-Adly said that al-Zawahri will stand trial soon. But he did not give a trial date, nor how long al-Zawahri had been in custody or who handed him over to Egypt.
Under Egypt's emergency laws, a suspect can be held without trial or charge indefinitely.
However, Egyptian law doesn't provide for a new trial for a suspect who has been convicted in absentia in a military court and returns to the country. It only permits clemency pleas to the President. El-Adly didn't explain how a retrial would happen.
Al-Zawahri's family members were surprised when they read a recent newspaper report about his whereabouts.
"It was a surprise, we didn't know if he was alive or dead," said Mahfuz Azzam, al-Zawahri's great uncle.
Azzam, a lawyer, wondered why Egyptian authorities had held him so long without telling his family or giving him access to legal help.
He said that Muhammad’s wife and six children are living in Egypt.
Azzam said he wouldn't represent Muhammad al-Zawahri himself in a retrial because he objects to civilians being tried in military courts.
It was not immediately clear why the government was acknowledging the detention now, though there have been Arab newspaper reports lately speculating that he died in police custody and that American intelligence officials were interested in getting hold of his remains for DNA sampling.
An Egyptian attorney who defended Muhammad al-Zawahri in the past says he was doing charity work in Afghanistan.
Those reports came as speculation was high that US authorities had captured or killed bin Laden and Ayman al-Zawahri. US military officials have denied capturing bin Laden and have said nothing about netting his deputy.
Montassar al-Zayat, a prominent Egyptian attorney who defends many Islamists, said Muhammad al-Zawahri is not known to have any ties to al-Qaida, though he had been a Jihad member for years. He spent time in Afghanistan in 1992-94 and again in 1996.
Al-Zayat, who defended Muhammad al-Zawahri in a 1999 trial, said he was sentenced on charges of membership in an illegal group, seeking to overthrow the Egyptian government by terrorist means, and was an accomplice in crimes to undermine the state.
Muhammad al-Zawahri, an engineer by profession, left Egypt in 1980 and is not known to have returned until he was brought into custody by the Egyptian authorities, said his family.
Al-Zayat said Muhammad al-Zawahri was in Afghanistan not as a fighter, but working with a Saudi-based Islamic relief agency, The International Committee for Islamic Relief.