Describing Tuesday's attack, the newspaper’s editor said: "Some men dressed in black broke into our office and opened fire", killing the editorial manager and a circulation assistant and wounding another employee.
"They were looking for three of our reporters but they managed to escape because our office is large," said N Vithyatharan, editor of the Tamil-language Uthayan newspaper based in the northern town of Jaffna, 300km north of Colombo.
Uthayan is an independent newspaper, but is considered to have close links to Tamil Tiger rebels fighting for a separate homeland for the country's ethnic Tamil minority.
"I have no doubts that this is a work of armed groups working with the government security forces," Vithyatharan said.
Liberation Tigers of Tamil Eelam rebels have fought the government since 1983 to create a separate nation for ethnic minority Tamils, accusing the majority Sinhalese-dominated state of discrimination.
"I have no doubts that this is a work of armed groups working with the government security forces"
Uthayan newspaper editor
More than 65,000 people were killed in the conflict before a Norway-brokered ceasefire was signed in 2002.
Peace talks later broke down, and the truce itself has been seriously undermined by growing violence.