"Two (Molotov) cocktails exploded at a mosque inside the BNS Issa Khan in Chittagong after the (weekly) jumma prayers... Six people received minor injuries in the blasts," the navy said in a statement hours after the blasts.
One person was detained from the scene with several "unexploded" bombs, police said.
The navy statement, however, did not say if authorities suspected any Islamist outfit or other groups for the incident but said "outsiders too come to the mosque to offer prayers" alongside the naval personnel.
A police officer had earlier told PTI that they seized two unexploded bombs from the scene and detained two people for interrogation while a bomb disposal unit was allowed inside the base on the shoreline of Bay of Bengal.
An unconfirmed report earlier suggested the blasts took place in two mosques inside the navy unit.
Witnesses said a huge number of police and elite Rapid Action Battalion (RAB) guarded the navy base while several fire engines were sent inside immediately after the blasts.
The blast inside a defence installation appeared to be the first of its kind in Bangladesh, which in recent months has seen several violent incidents, including attacks on foreigners, minority religious places and secular bloggers claimed by the Islamic State (IS).
The country in the recent period also witnessed attacks on a Shiite shrine in Dhaka in which two people were killed, and a Hindu temple in northwestern Dinajpur.
The attacks have alarmed the international community and raised concerns that religious extremism is growing in the traditionally moderate South Asian nation.
Police said they so far found militant Jamaatul Mujahideen Bangladesh (JMB) links at least to of the recent killings of a Japanese national in northwestern Rangpur and shooting of an Italian pastor in Dinajpur.
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