Controversial strongman Rajapaksa staged a dramatic political comeback on Friday, becoming the new Prime Minister after Sirisena sacked premier Ranil Wickremesinghe.
The sudden development came amid growing tensions between Sirisena and Wickremesinghe on several policy matters and the President has been critical of the Prime Minister and his policies, especially on economy and security.
As per rule, the president may appoint a new prime minister only under certain conditions such as the death of the premier, resignation in writing, or a vote of no confidence in parliament against the government for a listed set of reasons.
"Rajapaksa's return to high office without any justice for past crimes raises chilling concerns for human rights in Sri Lanka," Brad Adams, Asia director at the HRW, said.
The New York-based watchdog said the current Lankan government's "failure to bring justice to victims of war crimes under the Rajapaksa regime reopens the door for past abusers to return to their terrible practices".
Rajapaksa's administration was implicated in egregious violations during the final stages of the brutal civil war in the island nation and in suppression of freedoms of the media.
The HRW said military forces under Rajapaksa's authority attacked civilians and executed prisoners during the final months of fighting against the Liberation Tigers of Tamil Eelam (LTTE).
People with suspected links to the LTTE were subjected to arbitrary arrest, torture, sexual violence, extrajudicial killings and enforced disappearances. Journalists and activists critical of the then Rajapaksa government faced harassment, arrest and even physical attack, it said.
The LTTE had run a military campaign for a separate Tamil homeland in the northern and eastern provinces of the island nation before its collapse in 2009 after the Sri Lankan Army killed its supreme leader Velupillai Prabhakaran.
Since Rajapaksa was sworn in as prime minister, there have been reports that his supporters took over the state media.
"The media outlets, rights organisations and victims' groups...now fear a return to anxiety and fear...It is critical that governments that helped Sri Lanka's return to a much more rights-respecting government act to ensure those gains are not lost," Adams said.
Mangala Samaraweera, a senior member of Wickremasinghe's party and minister of finance and media, has described the recent political developments in the country as "an anti-democratic coup".