Egypt's National Council for Human Rights (NCHR) said on Sunday that 2,600 civilians, security forces and members of the outlawed Muslim Brotherhood died in violent acts from June 2013 to the end of 2014.
Of the 2,600 dead, the majority were Muslim Brotherhood members at 1,250, while 700 were security forces and 550 were ordinary people, according to a report issued by the NCHR.
Egypt's authorities have mounted a fierce crackdown on Islamists since the ouster of President Mohamed Morsi in July 2013 after mass protests against his rule.
For almost two years now, the post-Morsi government has been battling militant Islamist groups, including an Islamic State affiliate in the restive North Sinai, who have carried out deadly attacks against security forces.
The insurgency has claimed the lives of hundreds of police and army soldiers.
The semi-governmental NCHR also said that during that period, human rights' organisations estimated that 80 to 98 died in detention, either in police stations or prisons, describing it as a "return to the phenomena of people dying inside detention places".
However, the interior ministry only admitted to the death of 36 detainees.
"It is true that there is nothing that proves that any of them died from torture, but there is also nothing to prove otherwise," the report read.
The NCHR attributed the death of the detainees to "poor living and health conditions" as well as severe overcrowding in temporary detention centers in police stations and prisons.
The report said that the level of overcrowding, according to the interior ministry's statistics, had reached 400 percent in police stations and 160 percent in prisons.
The statistics reveal that "life inside these places is very difficult," the report added.
The report also stated that, between June 2013 and December 2014, detention periods for those awaiting trial were extended significantly, "making pre-trial detentions a punishment in themselves."
The NCHR called in their report for "an acceptable maximum detention period pending trials."
A law issued in November 2013 allowed Egypt's appeal and criminal courts to have no limits in ordering the detainment of defendants pending trial if the charges they face could result in a life in prison or death sentences.
The report also reiterated the council's calls for the amendment of the protest law.
The law, also passed in November 2013, mandates a three-day prior notification period to authorities before protests, and punishes anyone who fails to obtain a permit to up to three years in prison.
From 2013 to 2014, thousands of Islamists and other non-Islamist activists were sentenced to jail for periods ranging from one to three years for violating the protest law and protesting without a permit.
The recommendations of the NCHR are non-binding.
Copies of the report were submitted to President Abdel-Fattah El-Sisi, Prime Minister Ibrahim Mahlab and Minister of Interior Magdy Abdel-Ghaffar before its release to the public on Sunday.