Rafini announced the number of deaths in remarks broadcast on national television on Sunday from 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 suspected Islamist militants in the villages of Tchombangou and Zaroumdareye.
Niger has also seen forced killings between rival ethnic communities that have been provoked 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 resigning after a decade in power.
The ruling party’s candidate Mohamed Bazoum, who finished in first place, 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 are a serious threat to cohesion in communities, unlike any other.”
Bazoum will face former President Mahamane Ousmane in a second round, expected on February 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 face serious security challenges because of the evil campaign of non-discriminatory violence by terrorists in the Sahel, and only united action can help us defeat these vicious enemies of humanity,” Buhari said in Abuja on Sunday, according to a State House statement.
The United Nations strongly condemned the terrorist attacks, which “led to the killing and wounding of many innocent civilians.”
“I express my condolences to the Niger Mission to the UN and the people of Niger,” UN General Assembly President Volkan Bozkir said in a tweet on Sunday.
Secretary-General António Guterres said in a statement that he hoped the Nigerian authorities would “not make any effort to identify and speed up the perpetrators of this heinous act, while increasing the protection of civilians.”