Media rights groups said the blocking of www.srilankamirror.com and www.theindependent.lk violated basic rights guaranteed by the constitution. The government has already blocked at least eight news websites.
"We had news items criticising the government that would have been the reason for blocking our site," said Subash Jayawardene, editor of the www.theindependent.lk.
Sri Lankan authorities initially blocked news websites during and after the final phase of a 26-year war against separatists Tamil Tiger rebels, banning the rebels' main website in 2008.
The government is under heavy pressure to address rights issues and ensure media freedom after a U.S.-backed United Nations resolution was passed in March urging the country to prosecute war criminals.
"Our stories were credible and reported with responsibility. But the government may not have liked the stories we published," Kalum Shivantha, editor of the www.srilankamirror.com, told Reuters.
The websites were blocked by the state-run Telecommunication Regulatory Commission of Sri Lanka, which is overseen by Rajapaksa.
Officials at the commission were not immediately available for comment.
Media rights groups say least 14 Sri Lankan media workers have been killed since the beginning of 2006 and several media institutions have been attacked, but no one has been prosecuted.
Many media institutions are controlled indirectly by government proxies, media rights groups say.
In 2012 police raided and closed two news websites including www.srilankamirror.com, arresting nine people including eight journalists on charges of defaming Rajapaksa and reporting news in an "incorrect and vulgar manner". They were later released but their computers were confiscated.
Sri Lanka is ranked 165th out of 180 countries in the 2014 Reporters Without Borders press freedom index.
© Thomson Reuters 2014
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