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.
There was no immediate claim of responsibility.
Boko Haram, the Nigerian Islamist militant group, has stepped up cross-border attacks into Cameroon in recent weeks as Cameroon has deployed troops to the region, joining international efforts to combat the militants.
"I can confirm that the home of Vice Prime Minister Amadou Ali in Kolofata came under a savage attack from Boko Haram militants," Issa Tchiroma told Reuters by telephone.
"They unfortunately took away his wife. They also attacked the lamido's residence and he was also kidnapped," he said, and at least three people were killed in the attack.
A Cameroon military commander in the region told Reuters that the vice prime minister, who was at home to celebrate the Muslim feast of Ramadan with his family, 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 Colonel Felix Nji Formekong, the second commander of Cameroon's third inter-army military region, based in the regional headquarters Maroua.
The Sunday attack is the third Boko Haram attack into Cameroon since Friday. At least four soldiers were killed in the previous attacks. Meanwhile, some 22 suspected Boko Haram militants, who have been held in Maroua since March, were on Friday sentenced to prison sentences ranging from 10 to 20 years. It was unclear whether the events are related.
Boko Haram have killed hundreds of people this year, mostly in northeastern Nigeria, although they have bombed places across the country.
A bomb attack on a Catholic church in northern Nigeria's main city of Kano killed five people and wounded eight on Sunday, a senior police officer said. Churches have been a favourite target for the militants.
The attacker threw the bomb at worshippers on their way out of the church, police commissioner Adenrele Shinaba told Reuters. Police cordoned off the scene.
In a separate incident, a female suicide bomber tried to attack police officers on the streets. She killed herself but only wounded two of them, Shinaba said.