Police officials said the militants were members of the outlawed Jamaat-ul-Mujahideen.
The movement's supreme leader, Shayek Abdur Rahman, had already surrendered to security forces on 2 March.
Then on 6 March security forces captured Siddikul Islam Bangla Bhai, head of a second outlawed group called Jagrata Muslim Janata Bangladesh.
Authorities have since intensified the hunt, believing that only two more members of the Jamaat-ul's command council, or majlishe shura, are still at large.
The outlawed groups have been fighting for the introduction of sharia law in Bangladesh, a mainly Muslim democracy.
Officials identified the two remaining fugitives as Salahuddin and Saifullah and said they were the likely successors to Shayek and Bangla Bhai.
"We are frantically looking for these two," an intelligence officer from the elite Rapid Action Battalion said.
"If they are captured, we hope the Islamist militant activities will come to an end in the country."
Shayek is now in police remand for interrogation. Bangla Bhai is being treated at an armed forces hospital in Dhaka for injuries he suffered when he was captured.
At least 30 people have been killed and 150 wounded across the country in several bomb attacks since 17 August last year, but the government claims that the Islamist network has been effectively broken by the capture of the two key leaders.