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 percent of polls had opened within an hour of the set opening time, according to National Election Watch, a coalition of civil society groups.
Results are expected within about 48 hours of the vote.
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 party also alleged violence had taken place near several polling centers in Freetown on Saturday evening.
Two members of different international observer missions, speaking to AFP on condition of anonymity, confirmed one of the incidents.
Twelve men and one woman were contesting for president, but incumbent Julius Maada Bio's main challenger is Samura Kamara of the APC.
Bio, of the Sierra Leone People's Party, narrowly beat Kamara in a runoff in 2018.
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 percent 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 percent of valid votes for a first-round win.
Turnout has ranged between 76-87% over the past three elections.