Rafini announced the death toll in statements aired on national television on Sunday after a visit to the area 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 alleged Islamist militants in the villages of Tchombangou and Zaroumdareye.
Niger has also seen strong killings among rival ethnic communities that have been sparked by jihadist violence and competition for scarce resources.
Saturday’s attacks came on the same day the election commission announced the results of the first round of elections to replace President Mahamadou Issoufou, who is stepping down after a decade in power.
The ruling party’s candidate, Mohamed Bazoum, who finished 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 pose a serious threat to cohesion within communities different from any other.”
Bazoum will face former President Mahamane Ousmane in a second round scheduled for February 21st.
The president of neighboring Nigeria, Muhammadu Buhari, condemned the killings and described the incident as “another call for united action by African leaders against terrorism”.
“We face serious security challenges due to 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 of the State House.
The United Nations strongly condemned the terrorist attacks, which “resulted in the killing and injury of many innocent civilians.”
“I express my condolences to the mission of Niger to the United Nations and to the people of Niger,” UN General Assembly President Volkan Bozkir said on Sunday.
Secretary-General António Guterres said in a statement that he hopes the Nigerian authorities “spare no effort to quickly identify and bring to justice the perpetrators of this heinous act while improving the protection of civilians.”