Pastor Raymond Koh was abducted on 13th February 2017, less than three months after Amri Che Mat, a Shia Muslism, disappeared.
Benedict Rogers is from Christian Solidarity Worldwide (CSW) which has been campaigning for their release.
He told Premier's News Hour he was at the press conference where the news broke.
"There was a mood in the room that was on one level real shock but also real relief and people were pleased that the truth has come out.
"There was actually applause."
Over the past three years, several pastors and social activists have been reported missing in the Southeast Asian country.
In November 2016 a Christian couple, Joshua Hilmi and his Indonesian wife Ruth Sitepu, also disappeared.
A public inquiry into the disappearance of Pastor Koh was established by the Human Rights Commission in October 2017, and a similar inquiry into Amri Che Mat's case began in January 2018.
A panel published on Wednesday its 'final decision' on both cases, and concluded that there were several "common features" between the two cases.
Mr Mat was born and raised as a Sunni Muslim but according to the inquiry, "later took an interest in Shi'ism", which is illegal in Malaysia.
Both Mr Koh and Mr Amri had been investigated in the past for proselytising, which is a crime in Malaysia.
Rogers told Premier while the whereabouts of both the pastor and Mr Mat remains unknown; he hoped justice would be served.
"We very much welcome the recommendations of the inquiry - a whole range of recommendations including, firstly, the key point that freedom of religion or belief must be recognised as a fundamental human right for everybody," he said.
"But also recommendations for reform of the police, for those responsible to be held accountable, for there to be a special task force to fully and further investigate exactly who was behind this.
"And also a recommendation that Malaysia should sign up to international human rights covenants to better protect people. So I certainly hope and encourage the Malaysian government, which is a new government that took office a year ago since these disappearances,...to take these recommendations very seriously and to act upon them."
Listen to Premier's Eno Adeogun speaking with Benedict Rogers:
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