The incident occurred on Wednesday morning.
The terrorists stormed the village on motorcycles and headed for the mosque where they killed and injured the worshippers.
Ten others who were injured are currently receiving treatment in the Kontagora General Hospital.
The Niger State Commissioner of Police, Monday Bala Kuryas, confirmed the incident in a telephone interview.
He, however, said nine people and not 16 died in the attack, adding that additional security personnel have been drafted to the area.
A similar incident occurred some months ago when bandits killed 18 worshippers in Maza kuka village of Mashegu Local Government Council.
At least 30 passengers were burnt to death when gunmen suspected to be bandits set a bus ablaze on a road linking the Sabon Birni Local Government Area and the village of Gidan Bawa in Sokoto State on Tuesday.
President Muhammadu Buhari expressed sadness over the gruesome attacks on innocent travellers by terrorists.
The President’s reaction was contained in a statement issued by his Media Aide, Mr Femi Adesina on Wednesday in Abuja.
“I am very distressed at the manner of death visited on these hapless citizens who were undertaking a legitimate journey to another part of the country.
“It shows that the evil this administration is confronting is one that requires the support and involvement of all Nigerians,” he said.
The president extended deep condolences to the families of the victims, assuring that security agencies would continue to give their all to bring an end to the operations of the despicable people.
The Federal Government has designated bandits as terrorists.