The country's new fisheries and livestock minister, Narayon Chandra Chanda, announced the decision here, just a day after he assumed charge.
Bangladesh's Ministry of Commerce had banned the export of hilsa on August 1, 2012 due to its low availability.
Chanda said the ban appeared "largely futile" and so "we will export hilsa in official channel to stop its smuggling".
"Our hilsa production has (also) increased and there is demand in the international market so we want to move towards exports," Chanda told journalists.
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Chanda said despite the ban, hilsa fish was being smuggled out of the country and "as a result the government is losing out in taxes (and) if we allow exports it will open the way for legal trade and diminish smuggling significantly".
He said the government, however, will continue its conservation campaign particularly to protect the female hilsa.
Bangladesh's water bodies produce nearly 75 per cent of world's hilsa yield, while the country and last year the patent office named hilsa a "geographical indication product".
Hilsa is globally reputed for its unique taste but apart from the fish itself, its roe or egg tastes as good as, if not better than, caviar, one of the world's most cherished dishes.
Bangladeshi people are also known for their skill to cook hilsa in more than 50 ways with mustard, curd, brinjal, green banana, baking in young plantain leaves, smoke, fry, and so on.
Basically asea-water fish, hilsa makes its way up fresh water rivers travelling up to 1300-km during mating season, a feature that gives it the repute of being the most mobile fish species having its roaming ground both in sea and fresh water.