"The man is in intensive care in hospital" with serious head injuries, police spokesman Prishantha Jayakody told AFP, adding no arrests had yet been made.
At least six workers at the Jaffna-based Uthayan newspaper, including four journalists, have been killed since 2006 over its alleged pro-nationalist Tamil stance.
"This attack is aimed at scaring our employees so they will leave journalism," Uthayan's publisher E. Sarvanapavan told AFP.
The opposition Tamil National Alliance legislator said he believed the assault was in response to a recent sweeping win by his party in local council elections.
The council polls were the first held in the area since Sri Lanka inflicted a crushing military defeat on Tamil Tiger rebels, with whom the TNA was closely linked, in 2009.
"Attacking Kuhanathan is not the democratic way to behave in defeat. The paper's coverage gave equal coverage to the opposition and government," said Sarvanapavan.
Some 17 journalists and media employees have been killed in Sri Lanka in the past decade, with none of the murders being solved, according to rights groups.
"For too long Sri Lankan authorities have been indifferent about the targeted attacks, killings and disappearances," said the New York-based Committee to Protect Journalists (CPJ) in a statement.
"That must end," said CPJ deputy director Robert Mahoney.
Attacks against journalists and news outlets have continued despite the end of the decades-long war between the military and rebels, said Mahoney.
The latest assault came a day after police found the body of Pattani Razeek, a human rights activist who disappeared in 2010. The UN High Commissioner for Human Rights on Friday urged Sri Lanka to "expedite" investigations and prosecute those involved in the crime.UN records show 5,653 outstanding "enforced and involuntary disappearances" in Sri Lanka. Among those missing is freelance journalist and cartoonist Prageeth Ekneligoda, who vanished on the eve of the 2010 presidential polls.