Egyptian prime minister Ahmed Shafiq has apologised on television for fatal clashes in the centre of Cairo.
Up to 10 people have died during fighting in Tahrir Square between supporters and opponents of President Hosni Mubarak on Wednesday.
Mr Shafiq said on Thursday that those responsible would be punished.
But he has denied that government agencies were in any way responsible.
Mr Shafiq said the unrest had caused divisions that would take a long time to heal and promised a full inquiry in the events of the past days.
Rival factions are entrenching their positions in Tahrir Square.
Troops were previously criticised for not intervening in clashes there, but they took up positions on Thursday to separate the rival factions.
However, they were unable to control sporadic outbursts of violence.
There has been a constant stream of ambulances taking the wounded away.
The ministry of health says more than 800 people have been injured.
The protesters are demanding that Mr Mubarak, 82, who has ruled since 1981, step down immediately.
However, supporters of the president have pushed them out of some streets near Tahrir Square which they controlled.
The BBC reports that stones were thrown on both sides and some gunshots have been heard.
Announcements
In a TV address on Tuesday, President Mubarak said that he will serve out his current presidential term, which ends in September, but will not run for re-election.
State TV has now quoted Vice-President Omar Suleiman as saying Gamal Mubarak would also not now run for the post.
Former IAEA leader Mohamed ElBaradei and the Muslim Brotherhood have rejected government calls for negotiations, saying Mr Mubarak must leave office first.
If Mr Mubarak does not step down, demonstrators plan to march on the presidential palace on Friday.
Mr Suleiman says the government will not accept intervention in its internal affairs.
The United States and other countries say they want swift political change in Egypt.
But Mr Suleiman says intervention in Egypt's affairs is "strange, unacceptable and the government will not allow it."
Tensions are high in Alexandria after one of the country's biggest shopping malls was ransacked by looters.
Tanks are now parked in front of the mall to prevent people getting in.
Appeal for time
Vice-President Suleiman has appealed for time to carry out political reforms before the presidential elections in September.
He warned there would be a political vacuum if a proper period of transition was not allowed.
In an interview broadcast on state TV, Mr Suleiman said it was essential to keep existing institutions in place until September.
"The youth were demanding the abolition of the (parliament)," he said.
"That means we would be unable to look into the issue of constitutional reforms. There has to be a parliament so that these reforms can be looked into and studied and discussed...
"The September date is a necessity. We have to commit, we have to adhere to it, otherwise we will have a political vacuum."
Mr Suleiman also said the Muslim Brotherhood had been invited to talks.
"They're still hesitant to enter dialogue but I believe it's in their interests," he told state TV.
The BBC reports the party has previously rejected government calls for negotiations, saying Mr Mubarak must leave office first.
