Attackers wielding cricket bats forced their way into the offices of the Uthayan newspaper around 5 a.m. Wednesday after smashing distribution vehicles outside.
The newspaper's regional office, in Kilinochchi, around 60 miles southeast of Jaffna, was printing its latest issue when the attack came, the publication reported on its English-language website.
Two staff members needed hospital treatment for facial injuries, the newspaper's report said.
The owner of Uthayan, E. Saravanapavan, told the BBC that six staff members and a driver who had brought copies from the northern town of Jaffna for local distribution were in the office at the time of the attack.
Saravanapavan said six masked men burst into the office shouting in Sinhala, the language of the majority Sinhalese in Sri Lanka, and waving cricket bats.
"In the office the manager was sleeping on the floor. They hammered him," Saravanapavan told the BBC.
"Another boy was badly hit. He needed stitches between his ear and his jaw," said Saravanapavan who won a seat in Parliament as a member of the opposition party Tamil National Alliance.
The BBC said the newspaper's office in Jaffna has been attacked in recent years. Several staff members have been killed and in 2011 a senior editor fled the country after being severely beaten.
Journalists are often targets for violence in the ethnically divided island country of 20 million lying around 40 miles off southern India.
Around 15 million Sri Lankans are Sinhalese, mainly Buddhist and considered indigenous to the island, and around 2.5 million are Tamils of Hindi religion living mostly in the north.
Many Tamils have relatives in India's southern region, especially Tamil Nadu state across Paulk Strait, which separates the countries.
Despite the ending of a 25-year civil war in 2009, ethnic tension remains high because of issues and legal cases surrounding alleged war crimes and equality of job opportunity in central government for Tamils.
In 2009 the Sri Lankan regular army defeated the Liberation Tigers of Tamil Eelam -- the Tamil Tigers -- who were fighting a guerrilla campaign to create an independent Tamil state called Tamil Eelam in the north and east of the island.
Sri Lanka remains a dangerous place for journalists reporting on sensitive political issues, ranking 162nd out of 179 countries, the 2013 World Press Freedom Index compiled by Reporters Without Borders said.
Last month Reporters Without Borders said state-owned Sri Lanka Broadcasting Corp. is censoring FM retransmission of the BBC's Tamil-language broadcasts.
Censorship started March 16, a day after the start of the U.N. Human Rights Council's latest session which is looking at the issue of war crimes in Sri Lanka.
"The replacement of the BBC's coverage of the Human Rights Council's activities by completely unrelated programming is a direct violation of the Tamil population's right to information," Reporters Without Borders said in a statement with the press freedom group Journalists for Democracy in Sri Lanka.
"Those responsible for this censorship are also directly undermining the national reconciliation process, which has already been weakened by arbitrary control of news and information and by violence targeting journalists who try to cover this process."
In February United Kingdom Foreign Office Minister Alastair Burt urged Sri Lankan authorities to find the three attackers of a dual British and Sri Lankan nationality journalist shot in his home in Colombo.
Sunday Leader reporter Faraz Shauketaly, 52, was taken to a hospital for emergency surgery.
"There has been a range of attacks in Sri Lanka on journalists, civil society organizations and others in recent years," Burt said in a written statement.
"To date, too many incidents have had little investigation and no resolution."
Four years ago, Sunday Leader newspaper editor Lasantha Wickrematunge was shot dead by masked men on motorbikes.