Police spokesman Prishantha Jayakody said Bennet Rupasinghe, the Sri Lanka-based news editor of lankaenews.com, was arrested and remanded in custody until April 7.
"Mr Rupasinghe had allegedly threatened the brother of a suspect who is alleged to be involved in an arson attack on the website office," Jayakody told AFP.
The office, just out of Colombo, was torched in January and the editor, Sandaruwan Senadeera, blamed the fire on the government.
Senadeera fled to Britain after saying he had received death threats, and has alleged the arson attack was a concerted effort by the government to silence websites that do not support the administration.
"The situation for the media in Sri Lanka is going from bad to worse," Senadeera told AFP by telephone in January.
Another contributor to lankaenews.com, cartoonist Prageeth Eknaligoda, disappeared two days before the January 2010 presidential election in what is assumed to be an abduction case.
The lankaenews.com attack appeared sim