The magazine's anniversary edition dated February 6 had been held by the customs as it carried a 1987 interview of slain LTTE chief Velupillai Prabhakaran.
The Prime Minister had issued the directive after determining that the contents of the magazine did not pose a threat to national security.
He also advised the customs officials to be in touch with the Ministry of Media in order to arrive at such decisions in future.
The civil war in Sri Lanka came to an end in 2009 when the LTTE was finally crushed by the armed forces and the groups's leader Prabhakaran was killed.
The UN says 30,000 people were killed towards the end of the nearly three decades-long civil war in the country.
The LTTE remains proscribed in Sri Lanka and many other countries, including India, the US and the UK.

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