A former Anglican archbishop of Rwanda has challenged a claim by the Church of England that he endorsed the appointment of a priest in Worcestershire who is under investigation over accusations that he was complicit in the 1994 genocide.

As Rwanda prepares to mark the 20th anniversary of the start of the genocide tomorrow, the church said that Bishop Jonathan Ruhumuliza is on "special leave" while it looks into "disturbing" accusations, brought to its attention by the Observer in February, that he was a propagandist for the regime responsible for the murder of 800,000 Tutsis and was implicated in killings.

The Church of England has defended Ruhumuliza's appointment as a priest at St Mary and All Saints church in Hampton Lovett, Worcestershire, in 2005 by saying that it conducted "extensive checks" into his background and found no evidence of involvement in the genocide. It said the bishop was "commended" to it by the then archbishop of Rwanda, Emmanuel Kolini.

Kolini has told the Observer that he did no more than say that the Church of England might help Ruhumuliza out of humanitarian concerns. He said he warned the church that the conduct of the bishop and other clergy during the genocide had not been properly investigated in Rwanda because they had gone into exile.

"I did say they could help him as a human being. But I also said that the church in Rwanda had never sat down to discuss the issue of those bishops who have left Rwanda and who were in exile. I said it was for the Church of England to judge whether they could use him or not," he said.

"If the Church of England didn't know what happened in Rwanda and how bishops behaved who were in Rwanda then, I didn't want to spend much of my time on it instead of caring over the orphans and widows and the destroyed. My concern was to help the church in Rwanda, not spend much time on those who are on the run."

Ruhumuliza became a deeply contentious figure within the Anglican church in Rwanda because, with its archbishop, Augustin Nshamihigo, at the time he defended the genocidal regime to the outside world. Ruhumuliza wrote to the All-Africa Council of Churches and held press conferences saying the "government is trying to bring peace in the country" when the prime minister and members of his cabinet were touring Rwanda encouraging the killings.

Human Rights Watch later described the bishop as "acting as a spokesman for the genocidal government". London-based African Rights called him a "propagandist" and alleged that he worked with another bishop in refusing shelter to Tutsis facing imminent death and also exposed others to attack.

After the genocide, Ruhumuliza's actions led to a rift within the Anglican church in Rwanda as other clerics and worshippers refused to attend his services. He left the country shortly afterwards for Canada and then to serve as a bishop in Cameroon before moving to Britain.

The archbishop of Canterbury's office at Lambeth Palace responded to Kolini's assertion by saying that he sent it a letter in May 2005 in which "he stated that he found no reason not to commend Bishop Jonathan Ruhumuliza and wished him a fruitful ministry".

Kolini said he stands by his characterisation in his 2007 book, Christ Walks Where Evil Reigned, of Ruhumuliza and other Anglican bishops as "errand boys" for the genocide government. He said he has no knowledge of the "extensive checks" Lambeth Palace said it had made into Ruhumuliza's background.

Ibuka, the genocide survivors' association in Rwanda, has criticised the Church of England for failing to scrutinise Ruhumuliza's past closely enough when his record and the accusations against him were in the public domain.

Lambeth Palace declined to answer a number of questions about its checks on Ruhumuliza on the grounds that "the investigation is still going on". These included whether it was aware of the accusations against him in 2005 and, if not, how that fits with the claim to have conducted extensive background checks.

Chris McGreal's book, Chaplains of the Militia, on the role of churches during the genocide, is available from Guardian Shorts. Go to guardianshorts.co.uk to read an extract and find out more

• This article was amended on 7 April 2014. An earlier version of the headline said that the Church of England has suspended Jonathan Ruhumuliza while it looks into his alleged role in the Rwanda genocide. The Church of England has asked us to make clear that he has been placed on "special leave" by mutual agreement.