Mr Koh was kidnapped by masked men in the capital, Kuala Lumpur, in February 2017.
In a report released on Wednesday, the country's human rights commission (known as Suhakam) concluded that he was taken by Special Branch agents.
In response, Prime Minister Tun Dr Mahathir Mohamad conceded the country's Inspector General of Police (IGP) was implicated by the findings and a new IGP would have to be appointed before a fresh probe.
He was quoted by the New Straits Times as saying: "After that, we will set up a group to study whether there is substance in the hearsay evidence used by Suhakam."
The commission was also investigate circumstances around the disappearance of a Shi'ite Muslim activist. Amri Che Mat disappeared in November 2016. It concluded that, "on a balance of probabilities", police agents were responsible.
Police have previously denied involvement in either cases. But the commission concluded that there were "uncanny similarities" in the two cases.
It found both men had been under surveillance prior to vanishing.
Pastor Koh has been accused of proselytising to Muslims - which is illegal.
Malaysia's human rights commission, Suhakam, blames police Special Branch for the disappearance of Pastor Raymond Koh and Amri Che Mat.#AnglicanNews #Anglican #Anglicans #Ecumenicalhttps://t.co/Xt6eb0xqI7
— Anglican Communion News Service (@AnglicanNews) April 5, 2019
Human rights groups have raised concerns for religious freedoms among religious groups including Christians and Shi'ite Muslims in Sunni-majority Malaysia.
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