Rafini announced the death toll in statements broadcast on national television on Sunday during a visit to the area, near the Mali border. He did not say who was responsible.
Security sources said on Saturday that at least 70 civilians were killed in simultaneous attacks by suspected Islamic militants in the villages of Tchombangou and Zaroumdareye.
Niger also saw deaths in kind among rival ethnic communities that were fueled by jihadist violence and competition for scarce resources.
Saturday’s attacks came on the same day that the election commission announced the results of 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 first, expressed his condolences to the victims on Sunday.
The attacks, he said in a video he posted on social media, “remind us that terrorist groups pose a serious threat to cohesion within communities like no other.”
Bazoum will face former President Mahamane Ousmane in the second round, scheduled for February 21.
The president of neighboring Nigeria, Muhammadu Buhari, condemned the murders and described the incident as “another clarion call for united action by African leaders against terrorism”.
“We are facing serious security challenges because of the evil campaign of indiscriminate violence by terrorists in the Sahel and only united action can help us defeat these cruel enemies of humanity,” Buhari said in Abuja on Sunday, according to a statement from the State House.
The United Nations has strongly condemned the terrorist attacks, which “led to the deaths and injuries of many innocent civilians”.
“I express my condolences to the Niger Mission to the UN and to the people of Niger,” said UN General Assembly President Volkan Bozkir in a tweet on Sunday.
The Secretary-General, António Guterres, said in a statement that he hopes the Niger authorities “will spare no effort to quickly identify and present the perpetrators of this heinous act to justice, while strengthening the protection of civilians”.