Thursday also saw another hearing in the ongoing Al Jazeera trial where at least three journalists who worked for the network in Egypt are accused of "spreading lies" and aiding the now-banned Muslim Brotherhood group.
The report by CPJ comes from a survey taken on 1 June which estimates that at least 18 journalists are currently behind bars in Egypt in retaliation for their reporting. Most, it says, have been jailed after being accused of association with the Muslim Brotherhood.
"There are lots of journalists inside. All of them didn't do anything but their job," said journalist Baher Mohammed outside Cairo's Tora prison courthouse.
The CPJ estimates that at least 18 journalists are behind bars, including freelance photographer Shawkan who is yet to be charged since his arrest in August 2013.
"Journalists inside are treated very badly. Nowadays in the prison there is no water, food is not allowed," added Mohammed.
The report highlights a crackdown on freedom of the press, including reporting "black spots" in Sinai, an ongoing climate of self censorship due to government pressure, and direct censorship such as gag orders from the government.
"There is no press freedom in a country where there are journalists behind bars. Now, the situation of journalists in Egypt? There are still journalists behind bars, so no press freedom," Mohammed told RFI.
The Al Jazeera trial is set to continue on 29 June, with a verdict expected in the following session.