Barua, who headed the banned United Liberation Front of Asom's (ULFA) military wing, now leads a faction of the group opposed to talks with the Indian government.
ULFA for long has had bases and business interests in the Chittagong area.
Two of the convicts, Barua and former additional secretary Nurul Amin, were tried in absentia.
Two former generals also given the death penalty are then DG of the apex National Security Intelligence (NSI), Brig Gen Abdur Rahim, and former Directorate General of Forces Intelligence director, Maj Gen Rezzakul Haider Chowdhury, who later became the NSI chief.
All the accused were tried under the Arms Act for illegal possession of firearms and the Special Powers Act of 1974 for weapon smuggling.
The verdict came nearly a decade after the seizure of the weapons destined for ULFA hideouts in northeastern India through Bangladesh territory.
Around 1,500 boxes containing submachine guns, AK-47 assault rifles, submachine carbines, Chinese pistols, 840 rocket launchers, 27,000 grenades and 11.41 million bullets were seized from 10 trucks in the early hours of April 2, 2004.
Local media reported the weapons were smuggled from Hong Kong via Singapore.
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