The Communities Department said Qari Asim did not intend to "endorse" Khadim Rizvi when he published a statement on Facebook in 2017 apparently expressing solidarity with the controversial preacher.
A spokesman told the Mail on Sunday: "Imam Qari Asim did not intend that publication to be an endorsement of Rizvi and so took the article down, which he replaced with one calling for tolerance for all".
The response came after the newspaper claimed that the Leeds-based imam "supported" Mr Rizvi - a leader in Pakistan's Tehreek-e-Labbaik political movement.
The Islamist party staged violence protests last year following the acquittal of Asia Bibi - a mother-of-five who spent nine years on death row after being convicted of blasphemy.
A Catholic, Ms Bibi always denied the claim she insulted the Islamic prophet Muhammad following an argument with a group of Muslim women over a water cup. But hardliners demanded she be publicly executed.
Mr Asim, who is a member of the interfaith group Christian Muslim Forum, joined the Communities Department's Working Group on Anti-Muslim Hatred.
First established in 2012, the group advises ministers and civil servants on how to tackle Islamophobia.
In Eastern #Europe, meeting people from countries that have taken a large number of #Refugees, in recent years, learning about the social & economic impact on those countries #RefugeeCrisis #communitycohesion #socialmobility— Qari Asim MBE (@QariAsim) April 4, 2019
It is understood that Asia Bibi remains under the watch of security personnel in Pakistan - despite being acquittal last year.
Supporters hope she will soon be reunited with her children who have fled to Canada.
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