A local religious leader, or lamido, named Seini Boukar Lamine, who is also the town's mayor, was kidnapped as well, in a separate attack on his home.
The Nigerian Islamist militant group Boko Haram has stepped up cross-border attacks in Cameroon in recent weeks as Cameroon has deployed troops to the region, joining international efforts to combat the militants.
Government spokesman Issa Tchiroma said: "The home of Vice Prime Minister Amadou Ali in Kolofata came under a savage attack from Boko Haram militants.
"They unfortunately took away his wife. They also attacked the lamido's residence and he was also kidnapped." He also confirmed that three people died in the attack.
The vice prime minister, at home for celebrations connected to the Muslim month of Ramadan, was taken to a neighbouring town by security officials.
"The situation is very critical here now, and as I am talking to you the Boko Haram elements are still in Kolofata town in a clash with our soldiers," said the army's local commander Colonel Felix Nji Formekong, based in the regional headquarters Maroua.