The Ministry of Defence opposes a clause in Egypt’s draft constitution which prohibits the prosecution of civilians by military courts.

Mamdouh Shahin, a member of the military council and the Constituent Assembly, said the ministry opposed Article 62 because civilians who have attacked military personnel or property should be tried in military courts for “national security” reasons.

Shahin said he expected the assembly to agree with the ministry, especially after parliament cancelled Article 6 of the military law which had allowed the president to refer civilians for trials by military courts.

On Monday, the defence ministry sent a letter to the head of the Constituent Assembly, Hossam El-Gheriany, informing him of its reservations over Article 62.

Conflicts are ongoing over the text of the draft constitution, which was released in late October. Many factions have expressed their dissatisfaction with the draft, including liberal and leftist parties, judges, and the military.

In late September, Nasserist Hamdeen Sabbahi and reform advocate Mohamed ElBaradei called for a boycott of the assembly because it was “incompetent.”

The constitution-drafting body still faces the risk of dissolution by a court order because it was formed by the People's Assembly, the dissolved lower house of parliament. The court case that will ultimately decide the issue is ongoing.

Over 12,000 civilians, including children, faced military trials after the military council took charge of the country following the January 25 Revolution. Hundreds are believed to remain in prison, according human rights groups.

President Morsi ordered an amnesty for all political prisoners in early October, but the decision is yet to be fully implemented.