The move to switch the portfolios of foreign minister Mangala Samaraweera and finance minister Ravi Karunanayake was part of the first cabinet reshuffle by Sirisena, who is under fire over the performance of some of his ministers, since 2015, when he formed the coalition government in Sri Lanka.
Samaraweera, in addition to the finance department, will have the media portfolio. Karunanayake will now manage the foreign ministry.
He was also accused by them of facilitating international interference in domestic affairs through the 2015 resolution that was sponsored by the US, the UK and other countries.
Sri Lanka's Tamil community insist on having foreign judges and investigators for probing the alleged war crimes, claiming a lack of confidence in the country's judiciary.
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According to UN estimates, up to 40,000 civilians were killed during the three-decade-long war that ended in defeat for the Liberation Tigers of Tamil Eelam.
Karunanayake, 54, is an assistant leader of Prime Minister Ranil Wickremesinghe's United National Party (UNP). His handling of economy, particularly the raising of Value Added Tax, has been severely criticised.
Sirisena also took away the ports and shipping portfolio from legendary cricketer and former captain of the national team Arjuna Ranatunga and gave him the ministry of petroleum resources.
Ranatunga's handling of the ports ministry has drawn ire from trade unions. He reportedly angered both Sirisena and Wickremesinghe over his opposition to the proposed Chinese economic zone in the southern port of Hambantota.