Egyptian troops clashed with petrol bomb-throwing protesters against military rule in Cairo today, as the worst violence in weeks overshadowed the count in the second phase of a landmark general election.

At least 99 people were wounded as the soldiers repeatedly attempted to break up a sit-in outside the cabinet's offices demanding an immediate transition to civilian rule, state television reported.

The television also said 32 security forces personnel were wounded, including an officer hit by birdshot it said came from the protesters.

The clashes, which raged since dawn, were the bloodiest since five days of protests in November killed more than 40 people just ahead of Egypt's first parliamentary elections since the ouster of president Hosni Mubarak in February.

Violence erupted after a bloodied protester said he had been arrested by soldiers and beaten up, infuriating his comrades who began throwing stones at the soldiers, witnesses said.

Protesters also threw petrol bombs as the clashes continued through the morning with troops and military police repeatedly charging the crowd, AFP correspondents reported.

"The people demand the execution of the field marshal," they chanted in reference to Hussein Tantawi, the head of the Supreme Council of the Armed Forces, which took over following Mubarak's ouster.

Early afternoon, the military police pulled back to a side street but the demonstrators were pelted with stones by men in plain clothes from another government building and responded by smashing the windows of transport ministry offices.

Blogger Mostafa Hussein said demonstrators managed to reach the lobby of the cabinet offices after breaking down the front gate, but were pushed back by a large number of troops.

An AFP correspondent saw bloodied protesters being carried away by comrades and a string of arrests made.

Troops later released some of the detained demonstrators.

Leading activist Nur Nur, son of former presidential candidate Ayman Nur, emerged from behind the military police cordon limping and with a cut and large bruise to his head.

"When the military police rushed us, a girl behind me tripped up and fell," he said.

"I stopped to help her, and the soldiers beat us with sticks for about two minutes and then dragged us off into the parliament building."

A military official blamed protesters for the violence, telling AFP soldiers involved in the clashes had been tasked with protecting the cabinet and did not try to break up the sit-in.

Mohamed ElBaradei, the former UN nuclear watchdog chief turned dissident and presidential candidate, condemned what he said was a "savage" attempt to disperse the sit-in.

"Even if the sit-in was illegal, should it be dispersed in such a savage and brutal way, which in itself is a bigger violation of all laws and humanity," he asked on his Twitter account.

The Muslim Brotherhood's Freedom and Justice Party, which has dominated the parliamentary election so far, condemned "the assault on protesters and the attempt to disperse them."

It called on the military to protect the protesters from the men showering them with rocks from rooftops.

Tantawi, in a gesture apparently aimed at mollifying the protesters, ordered the treatment of all civilian wounded at military hospitals, which are usually better equipped than civilian counterparts, state television reported.

The demonstrators have been camped outside the cabinet offices since November 25, when they branched off from larger demonstrations in nearby Tahrir Square, the nerve centre of the 18 days of protests that led to the downfall of Mubarak.

They objected to the military's appointment of a new caretaker prime minister, calling on the generals to transfer power fully to a civilian government.

The military has said it will only step down once a president has been elected by the end of June following a protracted series of phased parliamentary polls.

The count was under way on Friday in the second stage of elections for the lower house of parliament. A third stage next month will be followed by a similar three-phase election to the upper house before the presidential vote.

As in the first phase last month, Islamist parties were leading the liberals, according to initial results, state media reported.

The flagship state-owned daily Al-Ahram reported a close race between the two main Islamist parties, the Muslim Brotherhood's Freedom and Justice Party and ultra-conservative Salafist movement's Al-Nur.

The main liberal coalition, the Egyptian Bloc, appeared to have garnered even fewer votes than it did in the first round, when it won about 13 percent, Al-Ahram reported.

The FJP, which was founded by the Brotherhood after Mubarak's ouster, won more than 36 percent of the vote in the first round, followed by Al-Nur's 24 percent.

The Muslim Brotherhood had been widely forecast to triumph as the country's best organised political movement, well known after decades of charitable work and its endurance through repeated crackdowns by the Mubarak regime.

The good showing by the Salafists has been a surprise, raising fears of a more conservative and overtly religious legislature.