The outlawing of the Brotherhood, mass trials and death sentences and a media crackdown have drawn fire too.
The official said concerns included a new law controlling demonstrations, "the lack of space for dissent, mass trials and death sentences".
Accusing the Egyptian government of employing a policy of "mass incarceration, mass trials and mass death sentences as a tool of political repression", the report cites figures suggesting that around 41,000 people are currently imprisoned for supporting pro-democracy movements.
But the US and EU governments sent only low-level officials to the Cairo ceremony in a sign of their reservations about human rights abuses, mass trials and repression that includes the proscription of the Brotherhood as a terrorist organisation.
"This does not prevent us from raising human rights concerns with the Egyptian government, including the use of mass trials, and we have consistently called for all trials to be conducted in line with international standards".
The presidential election led to the worst unrest in Iran since the 1979 revolution, but the protest movement has been silent for months, thanks in part to arrests, mass trials and intimidation.
"We had been parts of mass trials and got long sentences, even though there had been no evidence," said the inmate, who identified himself as Mourad Sarouf and said he had been falsely convicted of being a member of a group that planned attacks in Morocco.
"From mass trials and torture to death sentences handed down to political protesters and juveniles".
Judges have convicted hundreds of people at a time during mass trials, and many of them were sentenced in absentia.
Defence lawyers called the mass trial "farcical" and said many of those accused were not present during the clashes.
