FREETOWN, Sept 12 (Reuters) - Opposition leader Ernest Bai Koroma retained a comfortable lead in Sierra Leone's presidential runoff with just over half of votes counted, electoral officials said on Wednesday.

With returns in from 51 percent of polling stations, Koroma of the All People's Congress (APC) held 58.5 percent, ahead of Vice-President Solomon Berewa of the ruling Sierra Leone People's Party (SLPP) on 41.5 percent.

National Electoral Commission head Christiana Thorpe said authorities were investigating reports of irregularities and complaints from both political parties.

The elections are seen as a test for the former British colony's recovery from a 1991-2002 civil war which was largely financed by illegal diamond mining.

Full official results were expected to take several days, but both candidates' camps have alleged fraud and intimidation during Saturday's vote and each has already rejected results from certain areas they regard as biased towards the other.

Foreign and local election monitors have also reported some cases of electoral fraud, including apparent ballot stuffing.

The results dispute raised some fears of a return to the violence which sullied campaigning, when clashes prevented Koroma from touring the south and east, bastions of SLPP support -- exposing ethnic rifts that the victor will have to address.

Berewa has the backing of President Ahmad Tejan Kabbah, who is standing down under the constitution after two terms.

But his campaign was dealt a blow when Charles Margai, a scion of Sierra Leone's foremost political dynasty who left the SLPP in 2006, backed Koroma after finishing third in the Aug. 11 first-round. The opposition also won parliamentary polls held at that time.

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