Turnout was a crucial issue in Sunday's vote following the boycott call and the dramatic evacuation of Issoufou's challenger, Hama Amadou, suddenly flown from jail to Paris last week for medical treatment.
"The people of Niger have massively rejected this sham of an election," said the COPA 2016 opposition coalition, referring to poor voter turnout.
"The people responded positively to the boycott appeal," it said in a statement, calling on Issoufou to "draw the consequences of the people's will."
Issoufou, who won 48.4 percent in the first February 21 round, looked likely to clinch a second five-term against absent Amadou, who had won 17.7 percent the first time round.
COPA 2016 stopped short of calling on supporters to take to the streets in protest, but urged them "to remain vigilant and determined in order to turn this sanction against the regime into a victory for the people."
Voter turnout in the capital Niamey, an Amadou stronghold, appeared far lower, AFP reporters said, than the 66.6 percent turnout in February, when queues formed outside polling stations.
But Interior Minister Hassoumi Massaoudou on Sunday brushed aside the lack of voter enthusiasm in the capital, saying "Niamey is not Niger" and that national figures were "comparable or slightly lower" than in February.
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