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Sid'Ahmed Ould Deye said the complaints he had received had sown doubts in his mind - despite his own commission being satisfied with the election.
Official results gave victory to Gen Mohamed Ould Abdelaziz, who initially took power in a coup last year.
The opposition has said the poll was rigged and lodged complaints.
Overseas observers praised the poll's conduct but said the challenges should be investigated.
Mr Deye said he had resigned as a matter of "conscience".
"The complaints I received, as well as the contents of the challenges sent to the Constitutional Court, have sown doubts in my mind about the reliability of the election," he said.
On Sunday officials announced the general had won the poll outright with 52% of the vote, and put the turnout at 61%.
Defeated presidential candidates have been strident in their criticism of the general, calling the election a charade.