Two cases of ballot stuffing were reported out of nearly 25,000 polling stations nationwide in Wednesday's vote, he said.
"What we are describing are difficulties and anomalies, which is to say logistical issues that wouldn't have affected the credibility of the elections," Preda said at a media briefing in the capital Antananarivo.
African Union (AU) observers said the three leading contenders, all former presidents, "should show restraint and respect the law".
"It's not in their interests to act in a way that causes tension or trouble," said the AU's observer mission chief Ramtane Lamamra.
Presidential hopeful Rajaonarimampianina, who ruled from 2014 until September this year when he had to resign to contest the election, said on Thursday that there were "numerous irregularities" in the polls.
"We will not let the people be robbed of their vote," he warned.
Preda said that any irregularities which came to light should be investigated.
"It's important not to cheat. For me, people are attempting to cheat when they make (unfounded) allegations of irregularities, I don't like it," he said.
The former French colony has struggled to overcome political divisions after a disputed 2001 election that sparked clashes and a 2009 military-backed coup.
Rajaonarimampianina trailed on 4.38 per cent.
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