President Bio, 59, is running for a second term against 12 opponents. His biggest rival is All People's Congress' (APC) candidate Samura Kamara, who narrowly lost to Bio in the last election in 2018.
A provisional results sheet showed Bio had received over 1 million votes so far, compared with just under 800,000 for Kamara. Final verified results will be announced within the next 48 hours, the commission said.
The election has been tense. The APC said their election representatives were attacked and intimidated in three districts on election day. The election commission on Sunday outlined several instances where officials were beaten or intimidated.
The Carter Center, a U.S.-based election monitoring group, flagged reports "indicating a lack of transparency during parts of the tabulation process."
Sierra Leone's electoral commission said it would respond later.
Many Sierra Leoneans fear more unrest could occur as results are announced, particularly if none of the 13 candidates secures 55% of the votes cast, a situation that would trigger a runoff between the top two.
"Rest assured that I and the APC party would not and shall not accept any skewed, manipulated and unverified results," Kamara said in a statement on Sunday.
Schools, offices and most shops were closed in Freetown on Monday. Security forces had cordoned off the APC offices and surrounding areas.
Sierra Leone has been on tenterhooks since unusually violent protests broke out last year over rising prices. Bio and Kamara reported small-scale attacks on their supporters before the election.
Both sides have called for calm. But Kamara questioned the independence of election officials before the poll, expressing concerns about the possibility of vote-rigging.
Police fired tear gas at supporters gathered at APC headquarters in the capital Freetown on Sunday after the crowd turned rowdy, police said in a statement.
A Reuters reporter inside the building found a woman without a pulse lying in a pool of blood under a window with a fist-sized hole in it.
The police did not comment on what happened to the woman. An APC spokesperson said on Monday that she was a party volunteer and that she had died.
The European Union's election observation mission meanwhile said it was concerned about the "highly polarized political environment," and called for transparent vote-counting to build trust in the election process.