Local Leadership newspaper said the men shot dead were the secretary of Bama Local Government Council, Mohammed Salisu and a lecturer at southern Ekiti State University, whose name has not been verified.
The lecturer was said to be on a business trip to the city and decided to spend the town at Salisu's residence where the gunmen struck.
A neighbour who was interviewed by the newspaper, Simon Mishelia, said he was woken up by sound of gunshots in the middle of the night.
"I heard several gun shots in the neighbourhood but nobody was sure where exactly the sound was coming from until in the morning when we all realised that Salisu had been killed," he said adding that the remains of the victims were taken to mortuary by some police officers.
The commissioner of police for Borno state, of which Maiduguri is the capital, Abdullahi Yuguda, confirmed incident.
He said investigation by police commenced immediately after the attack took place.
An Islamic fundamentalist sect, Boko Haram, carries out frequent attacks in northern Nigeria.
The group has been waging a sustained war in Nigeria's northern cities in their bid to install an Islamic emirate in the country.
In several of the sects attacks, bombs, suicide bombers and drive by gun shots have been used to kill hundreds of people.
The oil rich African country has a population of 150 million equally divided among Christians and Muslims.
The Muslims are mostly found in the north while the Christians have their majority in the South.
Abuja: Gunmen killed two people including a local government secretary in Nigeria's northern city of Maiduguri where Islamic sect, Boko Haram has their enclave.
First Published: Wednesday, September 05, 2012, 15:46