Three armed men carried out the pre-dawn arson attack on the Uthayan office and printing press in Jaffna, the city and former war zone 400 kilometres (250 miles) north of Colombo, owner Eswarapatham Saravanapavan told AFP by telephone.
"Employees preparing to deliver the morning newspaper fled as the gunmen stormed in... It has to be either the government or para-militaries. Who else can carry firearms freely in Jaffna?" Saravanapavan said, adding there were no injuries but the printing press had been destroyed.
"Just last week we asked for security from the police after one of our offices was attacked elsewhere," he said, referring to a previous incident at another Uthayan office in the north.
There was no immediate comment from the authorities.
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Saravanapavan, who is also an opposition Tamil National Alliance (TNA) legislator, said he had lost at least five employees killed in attacks against the paper in the past eight years.
Saturday's assault came five days after the