The main financier of the group was one of those tried in absentia.
Egyptian authorities accuse the Muslim Brotherhood, which controls a fifth of the seats in parliament, of seeking to revive its underground military wing and of eventually trying to topple the regime.
Yusef Nada, a prominent member of the Brotherhood and one of those convicted in absentia, told Al Jazeera that the convictions would not change the Brotherhood.
He added that Hosni Mubarak, the Egyptian president, was attempting to prevent any opposition to his son, Gamal, from taking power.
"We were expecting it. But it is enough to know that it was in a military court so only the President can control it.
"He considers it [Egypt] a farm and a farm for his family.
"It will not move the Muslim Brotherhood one bit, but we only worry about the families of those convicted."
Essam el Erian, a Brotherhood member, said to Al Jazeera: "The whole case is a harsh case. The verdict is harsh compared to the accusation.
"And those people are innocent. About 30 people must be freed either now or after two months.
"It is a political tribunal, and [the defendants] are civilians who must be tried in front of a civilian court. This is a military court."
Police arrested 34 people after scuffles broke out amid protests and outside the Cairo court.
Police have also reportedly prevented family members of those on trial from entering the court.
Amr el Kahky, Al Jazeera's correspondent in Cairo, said that the protests had been quelled for the time being although police were outnumbered by protesters.
El Kahky said that the case was the first military tribunal to try senior members of the Muslim Brotherhood since 1922.
A large number of the group's leadership was on trial, including al Shater, the group's main financer. Businessmen who contribute money to the group were also tried.
El Kahky said: "The government is trying to blow the economy of the group and make sure they are not financed properly and do not carry out their plans."
Speaking to Al Jazeera, Kamal Helbawy, a former spoksman for the Muslim Brotherhood, said: "Taking some very prominent leaders... will affect the organisation to some extent but the Muslim Brotherhood is a big organisation and it has the ability to become solid again.
A spokesperson for the rights organisation Amnesty International, whose observers were prevented from attending the trial, said: "This trial appeared to be politically motivated from the start, when President Mubarak sent the defendants for trial before a military court despite an earlier civilian court ruling that some of them should be released.
"Today’s sentences leave little doubt that the Egyptian authorities are determined to undermine what has become the main opposition group in the country.
"Trying civilians before military courts, whose judges are serving members of the military, flouts international standards of fair trial and is inherently unjust, regardless of whether the defendants are allowed a right of appeal or not."
The defendants have been on trial since April 2006 with a verdict being repeatedly delayed.
The businessmen on trial had their assets frozen in February.
The defendants have no right of appeal as the trial was held in a military court.