The charges against the defendants were all connected with what the prosecution said was a plot to overthrow the government, including the assassination of political leaders such as President Hosni Mubarak and the destruction of public buildings.
Forty-three of the 94 defendants were acquitted in the trial, which started in November.
Since the attacks on the United States last September, the Egyptian authorities have taken a more aggressive stance towards Islamist groups, raising some concerns among human rights groups.
Fundraising
Those convicted in the trial will be unable to appeal against their convictions as the ruling by a military court can only be reversed by the president.
The defendants' lawyers had argued that the case was not backed by hard evidence, and largely based on confessions taken by the arresting officers.
Three of their clients, two Egyptians and a nation from the Russian republic of Dagestan, were sentenced to 15 years imprisonment, convicted of financing an illegal group to assassinate public figures.
Three others were given seven years in jail with hard labour, and the remainder were given sentences of between two and five years.
In addition to the coup charges, prosecutors also alleged that the defendants were involved in helping to fund Islamic militant groups abroad.
Their lawyers said they may have raised money for Islamic causes, including that of the Palestinians, but had not considered domestic attacks.
However raising money for charities without government permission is a crime in Egypt.
President Mubarak started referring civilians to military courts in 1992, in the wake of a violent campaign by Islamic militants to overthrow his regime.