Commissioner Fuwad Thowfeek told reporters at a pre-dawn press conference that he was going ahead with the second round according to a timetable agreed with all the candidates prior to yesterday's first round which was won by former president Mohamed Nasheed.
"We are going ahead with the elections on Sunday," Thowfeek said. "Changing the date will cause a lot of difficulties."
He added that voting will get underway at noon (0700 GMT), five hours behind schedule, but the 239,000 electorate will have eight and a half hours to cast their ballots.
The 53-member bloc's special envoy to the Maldives, Don McKinnon, said yesterday's presidential ballot was a "good election" even though it failed to deliver an outright winner and triggered a second round already scheduled for today.
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"It is important now that the electoral process move forward swiftly to its conclusion, with the holding of the second round," he said as the second placed Abdulla Yameen insisted he needed more time to face Nasheed in a run-off.
A second election on October 19 was also stopped by police saying Nasheed's opponents had not agreed to the voter lists as required by the Supreme Court.
The man who was thrown out of the run-off, resort tycoon Qasim Ibrahim, has already asked the Supreme Court to put off today's vote. The court has begun hearing the case.