The council called for an end to the state of emergency, which has been in force since 1981, saying it provided a loophole by which the authorities prevent some Egyptians enjoying their right to personal security.
The report was tougher than expected for a council set up and financed by the government.
But the human rights activists on the council have argued that anything less would damage the council's credibility.
The council was not able to carry out investigations of its own but by repeating allegations made by citizens in an official forum it implied it found many of them credible. Some parts of the report allege torture in general, without citing sources.
Rights groups say 2000 people
are detained without charge
The 358-page report describes in detail the deaths in detention of nine Egyptians during the year and calls them "regrettable violations of the right to life".
It also corroborated reports that the authorities detained large numbers of people in north Sinai, and tortured many of them, after bombings in Sinai resorts last October. Human rights groups say some 2500 people were arrested and that more than 2000 of them remain in detention without charge.
The council is chaired by Boutros Boutros-Ghali, former UN secretary-general and a former Egyptian deputy prime minister.
Hafidh Abu Siada, secretary-general of the Egyptian Organisation for Human Rights and a member of the council, said members close to the government had objected to the language in the report but eventually yielded to the activist group.
"We tried to write a report that is a real reflection of the human rights situation in Egypt," he told Reuters.
"Continuing the state of emergency is likely to spread among citizens a feeling of alienation and a temptation to stay away from participation in public life"
Egyptian Supreme Council for Human Rights report
The report says that up to thousands of members of Islamist groups have been in jail since the 1990s, even after they complete their sentences. Some detained without charge are not released after the maximum period of detention, it added.
On the detention campaign after the Sinai bombings, which the authorities have never explained in detail, it said: "Arbitrary detentions took place in north Sinai, where many detainees and their relatives were subjected to torture."
Citing reports which the council received during the year, it says that in Egyptian police stations suspects are given electric shocks, hung by their arms or legs from the ceiling or from doors, sprayed with cold water, made to stand naked in cold weather for many hours, or beaten with sticks, belts, electric cables, whips or rifle butts.
It said that it was normal investigative practice to arrest everyone around the scene of a crime and torture them to obtain information. Instruments of torture are usually readily available in police stations, it said, citing complaints.
The council spent the year asking government departments to respond to citizens' complaints, but the response was patchy.
The Interior Ministry, which runs the police force and the prisons, answered 27 of the 242 requests it received from the council. On torture allegations, it answered three out of 75.
The council's first recommendation is that emergency law be abolished rapidly so that people can take place "in an impartial and reassuring atmosphere" in a referendum on the constitution and in presidential and parliamentary elections later this year.
"Continuing the state of emergency is likely to spread among citizens a feeling of alienation and a temptation to stay away from participation in public life," it said.
The government has dismissed calls for the abolition of emergency law, saying it is needed to combat "terrorism" and drug trafficking. It has said it will not be used to obstruct opposition activities during the election period.
Abu Siada said another key recommendation was that President Hosni Mubarak issue a decree freeing detainees, especially those whom the courts have ordered released and those in bad health.