Rafini announced the death toll in remarks broadcast on national television on Sunday from a visit to the zone, near the border with Mali. He did not say who was responsible.
Security sources said on Saturday that at least 70 civilians had been killed in simultaneous raids by suspected Islamist militants on the villages of Tchombangou and Zaroumdareye.
Niger has also seen tit-for-tat killings between rival ethnic communities that have been stoked by the jihadist violence and competition for scarce resources.
Saturday’s attacks came on the same day that the electoral commission announced the results from the first round of the election to replace President Mahamadou Issoufou, who is stepping down after a decade in power.
Ruling party candidate Mohamed Bazoum, who finished in first, expressed his condolences on Sunday to the victims.
The attacks, he said in a video he posted on social media, “remind us that terrorist groups constitute a grave threat to cohesion within communities unlike any other”.
Bazoum will face former President Mahamane Ousmane in a second round run-off expected on Feb. 21.
The president of neighboring Nigeria, Muhammadu Buhari, condemned the killings and described the incident as “another clarion call for united action by African leaders against terrorism.”
“We are facing grave security challenges on account of the evil campaign of indiscriminate violence by terrorists in the Sahel and only united action can help us defeat these vicious enemies of humanity,” said Buhari in Abuja on Sunday, according to a statement from the State House.
The United Nations strongly condemned the terrorist attacks, which “led to the killing and injuring of many innocent civilians.”
“I express my condolence to the Niger Mission to the UN and the people of Niger,” said the UN General Assembly President Volkan Bozkir in a tweet on Sunday.
The Secretary-General, António Guterres, said in a statement that he hopes the Nigerien authorities will “spare no effort in identifying and swiftly bringing the perpetrators of this heinous act to justice while enhancing the protection of civilians.”