Najib also praised journalist Wong Choon Mei - who had written the report - as having shown "high values of professionalism" in claiming responsibility for the error. Wong had resigned yesterday.
Speaking to reporters at the Parliament lobby, Najib said he was satisfied with the apology issued by the news portal.
"I accept the apology or the decision to seek an apology by the editor of Malaysiakini on the publishing of the completely untrue manifesto that I (purportedly) issued.
"Secondly, I want to state that the journalist who resigned over the said article has shown high values of professionalism as she has demonstrated her responsibility (and) accountability for the story which is not at all true," he said.
"The question is the guilty quarters - the real culprits - behind the report are still hiding and we still do not know who is responsible for the said story,"Najib said.