The gunfight which occurred yesterday near the residences of members of the African country's parliament caused several injuries.
Two arrested members of the Boko Haram had led the security team in Abuja to a site near the residential compound for legislators where they said arms were buried.
"Some persons were injured and 12 others have been arrested in connection with the the incident. No sooner had the team commenced digging for the arms, they came under heavy attack by other Boko Haram elements," the spokesperson for the country's secret police, the state security service (SSS) said.
Boko Haram is fighting to install an Islamic emirate in northern Nigeria and impose strict Sharia law.
The oil-rich country's President Goodluck Jonathan had earlier declared a state of emergency in three states where the militants are very active.
Nigeria has 36 states and the country's population of over 150 million is roughly divided between a Muslim-dominated north and a Christian south.