The attack came after an earlier one which took place in Kano, where gunmen attacked worship services at a university campus church in northern Nigeria, killing at least 21 people in coordinated assaults that saw panicked Christians gunned down as they tried to flee.
Police spokesman Samuel Tizhe confirmed the attack and said officials would investigate.
Witnesses who declined to give their names out of fear the sect would target them said the gunmen stormed into the service and began firing. Most escaped, though as people came out of hiding later they found the pastor dead in a pool of blood in the sanctuary, witnesses said. Four other worshippers died in the attack, they said.
No group immediately claimed responsibility, but the attacks bore similarities to others carried by a radical Islamist sect known as Boko Haram.