The offices of Srilankamirror.Com and Lankaxnews.Com located in a Colombo suburb were raided and sealed, and documents and computers were seized from them.
The opposition United National Party (UNP) officials said the nine journalists included its editor and four women who were taken into custody by the crime investigation department.
Police told the website officials that the journalists were arrested for possessing 'anti-government' material.
The raid is yet another instance of crackdown on media in Sri Lanka where the government has shut down several independent news organisations and arrested journalists for 'anti-state' activities.
The government's media centre for national security, in a statement issued later, justified the raid and the arrest claiming that the websites concerned had carried out "malicious propaganda misleading both local and international communities against the state".
The government last year made it mandatory for website operators to register with the government information department, claiming that character assassination of individuals had been carried out by certain websites in violation of media ethics.
The access to four websites was blocked by authorities and later the issue was settled through court action.