Since the military deposed Mohammed Morsi in a July 3 coup, it has steadily intensified a crackdown on the Brotherhood, Egypt's largest political organization. Hundreds of its members are in detention and facing prosecution, many on charges of inciting violence.
Morsi himself has been held in an undisclosed location since his ouster. On Sunday, state prosecutors charged him with inciting the murder of his opponents. A date has yet to be set for the trial, in which 14 leading Brotherhood members are also charged.
In its recommendation to Egypt's administrative court, the panel of judges accused the Brotherhood of operating outside the law. It also recommended the closure of its Cairo headquarters.
The recommendation is nonbinding for the court, which holds its next hearing on Nov. 12.
Both state and private Egyptian media have adopted the interim government's line on dealing with the Brotherhood since the coup, repeatedly describing the group's actions and those of other Morsi supporters as acts of "terrorism."
The 85-year-old organization had faced legal challenges even before Morsi's ouster. Officially banned for most of its existence, it flourished as a major provider of social services to the country's poor and eventually won seats in parliament and union leadership.
But its lack of legal status, as well as its secretive organization and funding had left it open to recurrent crackdowns by the government over the years. Thousands of its members had been imprisoned on charges ranging from endangering national security to belonging to an illegal organization.
The Brotherhood rose to the forefront of Egyptian politics however after the 2011 popular uprising that forced longtime autocrat Hosni Mubarak from power. The group then formed a political party and won majority seats in the parliament. Its candidate, Morsi, became the country's first Islamist president.
The distinction between the religious-based Brotherhood and its political party however remained unclear, raising questions about financing and legal status and driving many opponents to file lawsuits seeking Brotherhood's dissolution.
A similar recommendation by a panel of judges was issued in March ahead of a court decision on the group's legal status. Only then, the Brotherhood declared it had registered itself as a non-governmental organization.
Critics questioned the hastened registration. Approval by the ministry overseeing such groups usually takes up to two months and requires review of applicants' records and accounting.
The non-governmental organization status also entails disengagement from political activities, such as backing candidates or campaigning before elections. Most observers doubted such a position would be possible for the Brotherhood, saying the distinction between the structure and funding of the group and its political party, Freedom and Justice, were opaque. Critics also charged that Morsi relied on the Brotherhood's leadership in his decision making.
Legal expert Nasser Amin said the court is likely to judge the Brotherhood in violation of the non-governmental organization status.
"It clearly had political programs and endorsed candidates in violation of the law," he said. "It also engaged in armed operations" when its members defended its headquarters building from protesters in a Cairo suburb at a time when nearly a half dozen Brotherhood offices were being torched.
At the time, Morsi blamed thugs for the political violence and accused the opposition of providing political cover for them. The largely secular opposition denied the charge, saying it did not condone violence.
Some in Egypt fear banning the Brotherhood and its political party would simply force it to again operate underground.
In a recent interview, interim Prime Minister Hazem el-Beblawi said such a ban would not be a solution. He also warned against taking such dramatic decisions during turbulent times, and suggested government monitoring of political parties as a more reasonable alternative.
Mohammed Zaree, a civil and political rights campaigner with the Cairo Institute for Human Rights Studies, said that although the Brotherhood's sudden registration as an organization left many questions unanswered, the current drive to ban it was more likely a move to appease a hostile public opinion and punish the group. Millions had demonstrated ahead of the coup demanding Morsi's resignation, accusing him and his group of abuse of power.
Doing so however would only drive it underground, Zaree said. "It was banned before. It never vanished ... Repression and security crackdowns never kill an idea – they only aggravate the problem."