The organisation was particularly concerned with recent harassment and reports of assault on journalists covering the the first round of Egyptian legislative elections on 8 November 2005.
The worldwide press freedom organisation called on the Egyptian authorities to carry out thorough and serious investigations into these events.
"We urge the authorities to see to it that the law is respected and that journalists are allowed to carry out news-gathering in complete freedom and safety," it said.
"Crude and brutal intimidation of journalists should have no place in Egypt. We also call on President Hosni Mubarak to act to halt this harassment," it added.
Reporters Without Borders also pointed out Aljazeera's Ahmed Mansour, presenter of the programme Bela Hudud (Without Borders), who was beaten by two men in front of his office in the Egyptian capital on the evening of 9 November.
After checking his identity, the two men beat him, breaking his glasses and leaving him with a neck injury before fleeing.
He said: "Two men approached me and asked if I am Ahmed Mansour. As soon as I replied 'yes' they started punching me in the face, which left me in shock and pain, with broken glasses and a bruised cheek and forehead.
Aljazeera show host Ahmed
Mansour was assaulted in Cairo
"I still had to face the viewers and my guest who was the chairman of al-Wafd, an opposition party candidate running in the current elections in Egypt."
When Mansour made his live broadcast 30 minutes later with his injuries clearly visible to viewers, he said: "Egypt should protect its honest sons."
Reporters Without Borders also mentioned attacks and harassment on several other Egyptian reporters.
The Egyptian government has not commented on the statement or the attacks on journalists.