Polling stations closed in Bamako, Mali, at 6PM UTC on Sunday (June 18) to begin vote tally.
During the day, citizens had voted on a new constitution.
Constitutional court supervisor Hamadoun Sissoko was content with the voting process.
"We didn't have any problems with our delegates or with the heads of the polling stations. Every time we go around, all we have to do is introduce ourselves as Constitutional Court supervisors, and they let you work with your delegate. We haven't had any problems. "
Some 8.4 million citizens were eligible to vote in the referendum.
The danger of jihadist attacks was a consideration in central and northern regions, meaning the vote was not held in some parts of the country, including the town of Kidal, a stronghold of former rebels.
A team of observers from civil society groups backed by the European Union reported that there were only a few voting issues in the polling stations to which they were deployed.
They also reported that more than 80 polling stations in Mopti, in the center of the country, were not open "due to insecurity".
The group said that a "terrorist attack" had disrupted voting in Bodio, but did not give further details.
In Menaka, a northern region contending with rebels linked to the Islamic State group, voting was limited to its capital due to insecurity, local elected officials said.
Political disagreement also reportedly prevented voting in some areas.
Turnout, typically low in the country of 21 million, will be seen as an indicator of the junta's ability to restore stability and generate popular enthusiasm for its agenda.
The head of a Bamako polling station was optimistic: "I don't think the participation rate will be low, Hamidou Nantié Bougoudogo said.
"That's my point of view. [...] I hope the rate will be as high as we'd like."
Transitional leader col Assimi Goïta who supports a yes vote in the draft constitution cast his ballot in the garrison town of Kati. He's said the new constitution will "pave the way towards a new, strong and efficient Mali, at the service of the population's well-being."
The junta had advertised the new constitution as the answer to Mali's inability to tackle its multiple crises.
Goïta who seized power in 2020 has vowed to return the country to civilian rule in 2024. He called the Malians to remain united whatever the outcome of the referendum.
Results are expected within 72 hours.