Many Liberians failed to vote in a presidential run-off in the West African state on Tuesday, observers said, some staying away for fear of violence and others following a boycott appeal by the opposition.

Incumbent Ellen Johnson-Sirleaf is almost certain to win re-election after her challenger, Winston Tubman, withdrew alleging fraud in the first round.

As many as two out of three voters may have stayed away from the polling stations on Tuesday, and a low turnout risks harming Johnson-Sirleaf's authority in a new term.

United Nations peacekeepers and Liberian security forces deployed across the capital after a day of clashes that killed two people. Voter turnout was thin throughout Monrovia with electoral workers often waiting idly for people to arrive at polling stations, Reuters witnesses said.

We have spoken to our observers across the country and the indication that we are getting is that turnout is very low, said Dan Saryee, head of the Liberia Democratic Institute, which is tracking the vote.

He said incomplete reports showed turnout could be as low as 25-35 percent.

The poll is the first locally organised presidential election since a civil war ended in 2003. It was expected to pave the way for new investment, but fears are rising it could instead usher in open-ended political turmoil.

Johnson-Sirleaf won 44 percent of the first-round vote. Tubman, who took about 33 percent and whose supporters include many of the country's unemployed ex-combatants, said he would reject the results of the run-off.

We told them we were not voting and they went ahead and placed our photos on the ballot papers. Not only CDC people boycotted but many Liberians were listening to us, Tubman told Reuters late on Tuesday.

On Monday, police fired tear gas to disperse hundreds of Tubman's supporters who had spilt into a major thoroughfare, and officers also fired live rounds when they stormed Tubman's CDC party headquarters.

The United Nations said two were killed in the clash.

U.S. President Barack Obama called on Liberian security forces to show restraint and allow peaceful protest. The international community will hold accountable those who choose to obstruct the democratic process, he said.

After voting in Fefee, her home town just outside Monrovia, Johnson-Sirleaf said she regretted the loss of life and promised an investigation.

Liberia is going to move forward. We will find a way to heal the wounds. We will also find a way to reconcile people, she said, vowing to make youth a priority of her mandate.

Liberia is one of the world's poorest countries and 14 years of war that ended in 2003 killed nearly 250,000 and left its infrastructure in ruins.

DON'T WANT TROUBLE

Johnson-Sirleaf's standing at home, where many complain improvements have come too slowly, is not always on a par with international praise for the recently-named Nobel Peace Prize winner.

She secured the backing of the third-placed finisher in the first round, former warlord Prince Johnson, ahead of the run-off.

Tubman has alleged three ballot boxes were tampered with and said he would only participate in a run-off if it were delayed by two to four weeks and if counting procedures were amended.

The October 11 first round was broadly accepted by international observers and regional bodies have criticised Tubman's boycott decision.

Analysts said a successful boycott would complicate the incumbent's next mandate, perhaps forcing her into dialogue with Tubman.

Instead of consolidation and construction, it will be a second mandate of justification and possibly power-sharing, said Lydie Boka, head of risk consultancy StrategiCo.

Liberia's iron ore and oil have attracted major firms including ArcelorMittal, BHP Billiton and Anadarko Petroleum and a smooth poll could entice more.

Many in Liberia are just hoping for peace.

We don't want any trouble. But monkey and baboon not getting along, said a Monrovia resident who called himself Tarr, using the nicknames Liberians have given the candidates.

(Additional reporting by Claire MacDougall; Writing by David Lewis; Editing by Robert Woodward)