The E.U. mission said the Independent National Electoral Commission (INEC) should improve in six priority areas, including removing ambiguities in electoral law, ensuring real-time publication of and access to election results and clamping down on electoral offences.
President Bola Tinubu won the disputed February vote, whose result is being challenged in court by his two main rivals.
"Shortcomings in law and electoral administration hindered the conduct of well-run and inclusive elections and damaged trust in INEC," said the report seen by Reuters on Wednesday.
"A lack of transparency and operational failures reduced trust in the process and challenged the right to vote," the report added.
The February vote was marked by the lowest voter turnout since the end of military rule in 1999.
The INEC was not immediately available to comment.
An INEC spokesman told local TV that the E.U. mission report was "unfair," adding that INEC's failure to upload presidential election results on time was caused by a glitch in its system.
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