Rain-soaked roads from recent storms also delayed getting ballot papers everywhere on time, she said.
It is the high monsoon season in western Africa and on Friday torrential rains hit the country, causing treacherous conditions on many roads in the capital.
Christiana Thorpe, the NEC chief, also acknowledged the delays and the slow pace of voting, saying that "there is bound to be some hiccups but everything will be fine soon."
"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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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.
Polls are due to close at 5pm.
In the southeastern cities of Bo and Kenema, local journalists reported that voting had started peacefully and orderly, but a few minutes later than official scheduled time.
At one polling station in the second city of Bo, 250km southeast of Freetown, a quarter of registered voters had already cast their ballots two hours after the polls opened.
"There are long queues throughout the country and the process seems to be well-organised and peaceful," Marie-Anne Isler, the chief European Union observer, said.
Solomon Berewa, the incumbent vice-president and ruling Sierra Leone People's Party (SLPP) presidential candidate, was forced to turn back on Saturday when he turned up at a polling station in Freetown, as crowds of impatient voters crammed the entrance, shouting "we want to vote," an AFP correspondent at the scene reported.
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 are 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 Ernest Koroma, leader of the opposition All People's Congress (APC).
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.