The attack was carried out by attackers believed to be members of the Al Shabaab militant group.
“Three people died on the spot. Two others have passed on while being taken to hospital,” a police source there told Capital FM News.
Among those killed was a prison officer who was in the restaurant.
The newly posted police chief for the region Charlton Mureithi, when reached on telephone said: “I have not been adequately briefed about this incident.”
There were no immediate reports of any arrest of the attackers said to have been four in number.
Attacks targeting civilians and security agents in restaurants and other areas have become the order of the day in the border town and neighbouring Mandera since October 2011 when Kenyan military forces crossed to Somalia to fight members of the Al Shabaab.