(Reuters) - The Muslim Brotherhood said on Friday its candidate was leading the early count in Egypt´s first free presidential election that exposed a rift in the nation between supporters of Islamists and backers of men who served deposed autocrat Hosni Mubarak.

The Brotherhood said Mohamed Mursi was ahead based on a small sample of results shortly after voting ended in an election that marks the final step in a messy and often bloody transition to democracy, overseen by a military council.

The overall result will not be clear for some time. But the well- organized Brotherhood had been expected to do well.

Egyptian television showed live footage of a methodical counting process from polling stations around the nation of 82 million, with judges watching. Such scenes were unthinkable under Mubarak, when votes were chaotic and rigged.

None of the 12 candidates in the race is expected to secure the more than 50 percent of votes cast to win outright. So Egypt´s 50 million eligible voters are likely to go back to the polls for a run-off between the top two on June 16 and 17.

Election officials said turnout in the first round was about 50 percent.

Among Mursi´s main rivals are the more secular-minded former Arab League chief and foreign minister Amr Moussa and Ahmed Shafiq, Mubarak´s last prime minister and who, like his ex-boss, was a former air force commander.

"We are confident that the next president of Egypt is Mohamed Mursi," said Essam el-Erian, a senior member of the Brotherhood´s Freedom and Justice Party which secured the biggest bloc in parliament after a vote that ended in January.

If Mursi makes it to the second round and goes on to win a run-off, it will put Islamists in a commanding position in the Arab world´s most populous nation, helping redraw the regional map after decades of repression by Mubarak and his predecessors.

Islamists have already swept to power in Morocco, Tunisia and Libya, and have had a influential role in a revolt in Syria.

CALM ATMOSPHERE

But Egypt´s next president still does not have a permanent job description because of a tussle over who writes the new constitution, and he could find his powers tempered by the generals, who are determined to retain their privileges and influence.

Voting was held in a calm atmosphere over two days, with polls closing late on Thursday. Monitors did not report any major infringements that would invalidate the vote, although some candidates grumbled about their rivals´ conduct.

Yet Egyptians seem increasingly polarized between those determined to block the return of men branded "feloul," or remnants of Mubarak´s era, and those worrying that Islamists will monopolize power. Others worry about both options.

"The revolution was stolen from us by the ´feloul´, the Brotherhood and the army. If Ahmed Shafiq or Amr Moussa win, the people will go out in another revolution," said Mohamed Kamal, a 32-year-old decorator, who cast his vote late on Thursday.

Kamal picked leftist candidate Hamdeen Sabahy, a dark horse in the race. Also contesting the vote is another Islamist, Abdel Moneim Abol Fotouh, who has sought to draw support from liberals and hardline Salafi Muslims.

Some fear a backlash on the street if Shafiq wins. He was driven out of the prime minister´s post by protests shortly after Mubarak was toppled. Demonstrators hurled stones and shoes at him when he voted in Cairo on Wednesday.

A page on Facebook, a medium used to devastating effect against Mubarak, was launched on Thursday that threatened a "revolution if Moussa or Shafiq wins".

But to supporters, Shafiq´s military background offers reassurance that he can restore order on the streets, a major demand of the population 15 months after Mubarak´s ouster.

(Additional reporting by Tom Perry, Yasmine Saleh, Marwa Awad and Samia Nakhoul; Writing by Edmund Blair; Editing by Xavier Briand) (© Thomson Reuters 2012. 05/24/12)