Women were beaten and sexually harassed, and some said they filed complaints with Egypt's Interior Minister and Cairo's police chief.
Egypt's Information Ministry said late on Saturday it lamented two incidents in which reporters were hurt when they were caught between groups of fighting protesters, who, it said tried to mar the balloting despite a government ban on demonstrations.
The Egyptian Organisation for Human Rights said it filed a complaint with Egypt's Prosecutor-General Maher Abd al-Wahed, asking him to hear testimony from reporters who said they were attacked while covering the protests.
The group provided names of eight journalists it said had been attacked by security men, including a woman reporter who said she was beaten up as police watched.
The rights group is urging the prosecutor to bring the culprits to court.
The Information Ministry said eight members of Mubarak's National Democratic Party also filed complaints alleging they were beaten up.
Egyptians voted in a referendum on Wednesday to approve a constitutional amendment allowing for multi-candidate presidential elections. The government has declared the referendum, which passed easily, a success.
But in the lead up to the vote opposition groups called for a boycott and organised anti-Mubarak demonstrations.
"Those thugs were taking orders from high ranking officers. They didn't even have mercy on veiled women, they stripped their headscarves off ... You wouldn't know how to stop all those hands attacking you and touching your body"
Small groups of protesters were set upon by gangs of men chanting pro-Mubarak slogans. The beatings took place in full view of plainclothes security men and uniformed Egyptian police.
In some cases the police shouted instructions and formed cordons around protesters so the gangs could beat them without interference.
Three senior NDP members and high ranking security officers were seen at the scene of the clashes, activists said.
Lawyer Rabaa Fahmy said she was sexually harassed and that she recognised her attacker, grabbing him by his shirt to report him to police, but instead of arresting him, she said the police beat her up and let him go.
"Those thugs were taking orders from high ranking officers," Fahmy said.
"They didn't even have mercy on veiled women, they stripped their headscarves off. It starts with just one pulling you. Then the rest follow and you wouldn't know how to stop all those hands attacking you and touching your body."
Husni Mubarak has ruled Egypt
unopposed for 24 years
Journalist Nawal Ali filed a complaint against the Cairo police chief and senior members of the ruling party for ordering an assault against her, said Ibrahim Mansour, a member of the Egyptian press syndicate.
Egypt's prosecutor-general's office said it was investigating Ali's complaint, saying that journalists asked about the incident said they could not identify attackers who tore Ali's clothes, took away her bag and stole other belongings.
A medical examination showed Ali sustained a bruise and minor scratches, the prosecutor's statement said, as carried by the semiofficial Middle East News Agency.
Freelance journalist Iman Taha has been in hospital since Wednesday where she remains under examination after a violent sexual assault, said her lawyer Wafaa al-Masri.
"Whenever she leaves the hospital, we will file a complaint against not only her attackers, but also the police who prevented her from reaching an ambulance or seeking medical help for hours," al-Masri said.
New York-based Human Rights Watch asked Mubarak to form an independent judicial panel to investigate what it called "state-sanctioned brutality".
"I went through ... the various media coverage both in the United States and elsewhere, and I believe it is unfair and unjustified"
"The police and ruling party assaults on pro-reform advocates yesterday shows just how hollow the Mubarak government's rhetoric of reform really is," said Joe Stork from Human Rights Watch.
Reporters Without Borders, an advocacy group for journalists, said it was shocked by the number of assaults on female journalists committed "under the noses of secret service members".
"We strongly condemn these squalid assaults, unworthy of a democracy," the group said.
Journalists and activists met later on Saturday and said they plan to sue Egypt's Interior Minister Habib el-Adly for the police aggression.
"The Information Ministry, believing in the vital role that the reporters play to cover the different events, stresses its willingness to provide all the facilities and help that enable journalists to carry out their mission," it said Saturday.
However, Egypt said on Saturday that attacks on activists opposing this week’s referendum had been overplayed by the media, but that such attacks were unacceptable.
have been accused of thuggery
"I went through ... the various media coverage both in the United States and elsewhere, and I believe it is unfair and unjustified," presidential spokesman Suleiman Awad said on Saturday.
"When you have more than 54,000 electoral units nationwide, [and] when you have two sad, unacceptable incidents taking place in the greater Cairo area, this is not something to be exaggerated in the way some circles did," he added.
Awad said public prosecutor Maher Abd al-Wahed was investigating complaints by victims of clashes during the referendum, adding that anyone had the right to submit a complaint.
Asked if there would be arrests, Awad said: "This is something to be decided by the judiciary."