Police said the Jaffna office of the 'Uthayan' newspaper had come under attack around 5 AM (local time) today.
Two unidentified men stormed the office and chased away the security staff.
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"We have started an investigation", police spokesman Buddhika Siriwardena said.
"Just last week we asked for security from the police after one of our offices was attacked elsewhere," the paper's owner E Saravanapavan said.
Uthayan's distribution office in Kilinochchi in the north was also attacked on April 3.
Reacting to the incident, the government's national security spokesman, Lakshman Hulugalle said, "The investigation has revealed that setting fire to 'Uthayan' was an inside job to tarnish the good image of the government".
The Tamil paper known for its Tamil nationalist content has come under attack several times in the past during the LTTE's separatist campaign.
In February, a journalist working for a private weekly in Colombo was shot and wounded by an unknown attacker.
There is no state censorship in Sri Lanka, but rights groups say the media practices self-censorship to avoid provoking violence.
A total of 17 journalists and media employees have been killed in Sri Lanka in the past decade which saw the end of the island's brutal three-decade-long civil war when the army finally crushed the LTTE in 2009.
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