EC President Fuwad Thowfeek said the turnout was much lower than in the annulled September 7 election.
"Last time, a large number of people queued in the beginning. But we have no way of knowing the numbers on queue this time around. From the broadcasts on TV channels, we know that the number is lower," he said.
Polling officially ended at 3.30 pm local time for the 239,105 eligible voters, but many were still waiting in queues to cast their ballot, local media reported.
If no candidate gets over 50 per cent of votes in today's balloting, a run-off will be required between the candidate who receives the maximum number of votes and the runner-up.
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Today's polls is the Maldives' third attempt to elect a president in as many months. The country needs to have a new president in place by November 11 when the incumbents term ends.
However, EC member Ali Mohamed Manik told news portal Haveeru that JP is yet to sign any lists for the run-off, while PPM has stopped signing them today.
"If there has to be a second round, it is to be held tomorrow. However, we are facing some obstacles," said Thowfeek.
Former President Mohammed Nasheed's Maldivian Democratic Party (MDP) issued a statement "congratulating the people of the Maldives for peacefully and patiently voting in the new first round of presidential elections. The Maldivian people have, once again, shown their unrelenting commitment to democracy".