He was re-elected to Parliament at the 2000 parliamentary election and retained his ministerial portfolio. He was re-elected at the 2001 parliamentary election but the PA lost the election.

Besides serving as Health Minister, he also served as the Acting Defence Minister on several occasions.  During the height of the civil war, Sirisena said he was a soft target for the Tamil Tiger rebels with the separatists trying to assassinate him on at least five occasions.  

In 2008, Sirisena escaped unhurt when a convoy he was part of was attacked by a Liberation Tigers of Tamil Eelam's suicide bomber at Piriwena Junction in Colombo. One person was killed and seven injured in the attack.