Tallying, which consists of adding up counted ballots from each polling unit at the regional level, would take place in the capital Freetown, Bo, Kenema, Makeni and Port Loko, the commission said.
On Saturday, Sierra Leoneans voted in presidential, parliamentary and local elections, with many polling stations opening late in the capital.
But elsewhere in the country, more than 90% of polls had opened within an hour of the set opening time, according to National Election Watch, a coalition of civil society groups.
The West Africa Network for Peacebuilding, another observation group, said in a midday update Saturday that voting had been "relatively peaceful" - as did the electoral commission in a late afternoon statement.
But after polling stations began to close, the electoral commission said polling staff had been attacked by members of the public in certain area as they attempted to move materials.
Senior members of the main opposition All People's Congress (APC) party also alleged violence had taken place near several polling canters in Freetown on Saturday evening. Two members of different international observer missions, speaking to AFP on condition of anonymity, confirmed one of the incidents.
Rising food prices are a key issue for many in the import-dependent West African nation of eight million people. Year-on-year inflation hit 43 % in April, according to the latest official figures.
Some 3.4 million people were registered to vote, 52.4% of whom are under 35 years old, according to the electoral commission.
Presidential candidates must secure 55% of valid votes for a first-round win. Turnout has ranged between 76 and 87% over the past three elections.
Voters will also elect members of parliament and local councils under proportional representation after a last-minute switch from a first-past-the-post system. Under a recently passed gender act, one-third of all candidates must be women.
A new 11.% vote threshold will make it difficult for independents and minority parties to secure seats in parliament.
Many Sierra Leoneans vote based on regional allegiances, with jobs and benefits commonly perceived to flow to regions whose politicians are in power.
A June 14 poll by Institute for Governance Reform (IGR), a partner of the pan-African survey group Afrobarometer, forecast Bio will win 56% of the vote, with 43% for Kamara. Another poll, conducted by the newspaper Sierra Eye and two local data groups, forecast 38 percent for the incumbent and 25 percent for his main challenger.
The elections are being closely followed in West Africa, a region recently dominated by coups and turmoil.