Police said the Jaffna office of the 'Uthayan' newspaper had come under attack around 5 am (local time) today when two unidentified armed men stormed the office and chased away the security staff.
They then set fire to newspapers and news print reams.
Gun shots had been fired at the main printing machine, police said.
"We have started an investigation", police spokesman Buddhika Siriwardena said.
Uthayan's distribution office in Kilinochchi in the north was also attacked on April 3.