Mark Lipdo, director of the Stefanos Foundation, made the comments following a report from Human Rights Watch, which claims Nigerian women are being are forced to marry and convert to Islam as well as enduring physical and psychological abuse, forced labour and rape.
Speaking on Premier's News Hour, he said: "The Church at the moment is in confusion...the Church kept calling attention to the government to the whole issue [of persecution], and the situation fell on deaf ears.
"It got to this point where violence is institutionalised, and yet the situation is under denial.
"The Church sees it as a war against Christians, and they're not given the right to even define it as such."
Human Rights Watch interviewed 46 women who have either been abducted by Boko Haram and escaped, or have witnessed abductions.
It says the extremists target students and Christians, in particular. The group threatens victims with whipping, beating or death unless they convert to Islam, stop attending school, and agree to wear a veil or hijab.
Boko Haram translates roughly from the Hausa language as "Western education is forbidden".
Boko Haram abducted 276 schoolgirls from a secondary school in the predominantly Christian area of Chibok, Nigeria, in April.
The Nigerian government recently agreed a ceasefire with Boko Haram in an attempt to secure the release of the schoolchildren and other captives.
There have been reports that some schoolchildren have escaped; however, Boko Haram has not officially announced the release of any of the girls.
Mark Lipdo, director, Stefanos Foundation: