State elections are fiercely contested in Nigeria where governors are powerful figures and clashes, killings and voter intimidation are common.
Tense political rivalries played out in the southern state of Bayelsa state, Imo in the southeast and Kogi in the center of the country.
The electoral commission said one of its officials was abducted — while monitoring groups said two people were shot — including a man allegedly running off with a ballot box.
Counting began in the afternoon and election results were expected later on Saturday.
The voting took place amid sweeping travel restrictions and the police deployed helicopters and gunboats, while the army sent troops to "reinforce security."
On Friday, the Independent National Electoral Commission (INEC) said an official was "abducted while waiting to board a boat" in Bayelsa, while another boat carrying election documents capsized — affecting more than 5,000 voters.
Observers were watching the commission closely after the presidential election in February this year, when critics and the opposition said delays uploading results and technical problems created opportunities for rigging votes.
INEC said it had "done everything possible to guarantee that the weekend's election is free, fair, and credible."
The commission said it was investigating reports of vote tampering in Kogi state.
The civil society Transition Monitoring Group said a man was shot in Anyigba, Kogi state, after allegedly trying to "disrupt the election by snatching the ballot box." It shared footage of a bloodied body on social media.
The police have not responded to AFP's request for confirmation.
The Center for Democracy and Development (CDD) — a nonprofit organization focused on promoting democracy, peace and human rights — which observed the polls — said a person was shot in Famgbe, near Bayelsa's state capital Yenagoa. It did not provide further details.
The CDD warned of low turnout at certain polling stations, saying some people were "scared of coming out to vote due to fear of violence."
It also described widespread vote-buying, with some people exchanging their ballots for handouts of rice.
In Imo state, local media reported scuffles as votes were collected.
The governing All Progressive Congress, or APC, state governor is facing intense criticism from Nigeria's main labor union, which has threatened to call a strike after claiming Imo authorities were behind an attack on its leader last week.
Kogi state, led by the APC, was seeking to avoid a repeat of 2019 polls, which saw deadly violence and electoral malpractice.
The 2019 vote in Bayelsa was also blighted by violence and abuses including killings, abductions and intimidation.
Gift Meeting, a caterer in Yenagoa, told AFP the election was "not worth anyone dying for."
She said she believed the People's Democratic Party (PDP), in power in the state, but in opposition nationally, will win comfortably.
Nigeria has a long history of electoral violence since the country emerged from military rule in 1999 and many vote results ended up challenged in the courts.