At least six people were detained by police for showing their marked ballot cards as well as other misdemeanors such as attempting to offer bribes and obstructing the police, Xinhua reported.
Observers have also noted that the turnout has been less than expected.
"We have received 25 complaints about the voting process," Elections Commission member Mohamed Farooq told reporters.
"Our aim is to secure 65 seats in the parliament," Maldives President Abdulla Yameen told reporters after casting his vote.
"If we secure the majority in this election, we will prioritize bills on economic development and the amendment of the penal code. Our coalition is not going to fall apart after this election," he added
His main rival former president Mohammad Nasheed who heads the Maldives Democratic Party and currently has a majority in parliament was also upbeat.
"The elections are being held after consulting the committees that were formed to instruct and advise the Elections Commission. I believe - God willing — the election will be fair and will proceed without disruptions," former President Nasheed said after voting.
There are 85 candidates contesting from the opposition Maldivian Democratic Party (MDP); 50 from the ruling Progressive Party of the Maldives (PPM); 28 from the ruling government's coalition partner Jumhoory Party; seven from the government's coalition partner Maldivian Development Alliance (MDA); 12 from religious conservative Adhaalath Party; six from the Dhivehi Rayyithunge Party (DRP) and 114 independent candidates.
Capital Male has the largest number of constituencies at 13, with seven in Addu City and the remaining 65 constituencies scattered across the island nation.
The run-up to the elections have been steeped in controversy after the Maldives Supreme Court earlier this month handed down suspended prison sentences to the elections commissioner and his second-in-command.
The controversial ruling also removed the two from their posts leaving a virtually headless commission to oversee the parliamentary election. The Supreme Court March 9 issued a suspended six-month prison sentence to Elections Commission Chair Fuad Thaufeeg and declared void the membership of the commission's chair and vice chair.
The prison sentence has been suspended for three years.
The Maldives Supreme Court has repeatedly come under fire from the international community for failing to meet international standards and has been accused of attempting to undermine the independence of the Elections Commission.