The lankaenews.com premises were torched in a pre-dawn attack but there were no reports of casualties, a police officer at the scene told AFP.
Monday's attack appeared similar to the July burning of a private television station, Siyatha, in Colombo.
In January 2009, another independent television station, Maharaja Television, was bombed by an unidentified group of people.
A spokesman for President Mahinda Rajapakse's office said he had ordered police to carry out a thorough investigation.
Sandaruwan Senadeera, the editor of Lanka E-News, which supported the main opposition candidate Sarath Fonseka at the January 2010 presidential election, is based in Europe following death threats.
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"A group of unknown personnel had broken into the premises and set it on fire. By now everything that was inside the building has been destroyed," Lanka E-News said in a posting on its website.
A total of 17 journalists and media employees have been killed in Sri Lanka in the past deca