Al Jazeera's Greg Norman, at a polling station in the capital Freetown, said the centre did not open until about 10:15am.
"It's all looking a bit chaotic. Polling is really slow because there's no police at all here," he said.
One voter, Phillip Namara, 38, told Al Jazeera: "They're not allowing me to vote, they're not allowing me to exercise my rights."
After arriving at the centre and being assigned his voter registration card, Namara said he was told to go to another polling station.
At the second centre, they told him they did not have his information and to return to the first station. When he was again told his registration could not be verified, Namara decided not to vote.
Ernest Koroma, the leader of the opposition All People's Congress, told Al Jazeera the election was a "very good day for Sierra Leone".
Koroma said he was confident of victory even if there was a further run-off vote to decide the presidency.
"We have also made substantial inroads. We have been welcomed in areas that are not normally our strongholds. I am confident of victory - even if there is a run-off I am going to win."
European Union election observers, however, expressed satisfaction with polling.
"I hope the people of Sierra Leon can have this election without violence. All that is needed is one act of violence to spark another civil war."
Tom Dougherty, Atlanta, USA
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"For the moment, there has been no problem," Marie-Annie Isler Beguin, the chief EU observer, said in Bo, Sierra Leone's second largest city.Impatient voters
"But it's not only the election day which is important, but also how the political parties will handle the results," she said.
Counting got under way immediately after the polling stations had closed and complete preliminary results were expected by the end of next week.
Isler Beguin said that reports from across the country showed there had been no major incidents that could affect the vote.
"The information we have is that it has been OK, of course with little events, minor events, but nothing major," she said.
In one minor incident, Solomon Berewa, the incumbent vice-president and ruling Sierra Leone People's Party (SLPP) presidential candidate, was forced to turn back when he turned up to vote, as crowds of impatient voters blocked the entrance to the polling station.
Officials at the centre had to hold up the empty ballot boxes, which had just been delivered, to appease the crowd outside, who accused them of ballot stuffing.
About 2.6 million voters were eligible to pick a new president and MPs, six years after the end of the Sierra Leone's brutal civil conflict.
Ahmad Tejan Kabbah, the outgoing president who led the country for two five-year terms during and after the war, is not eligible to stand but has backed his vice president.
Seven political parties are fielding candidates, but the real battle is between Berewa and Koroma.
If none of the presidential hopefuls secures at least 55 per cent of the ballots cast a second round of voting will be held within two weeks.