Premier has confirmed the news with Festive, a Christian charity which supports Christian unions in sixth-form and Further Education.
Festive confirmed it is working with the Christian union which has been barred from meeting, but refused to name the group or college involved as it prefers to keep casework confidential.
The Christian union told Festive the college barred it from meeting because of the government's Prevent strategy.
Prevent is one of the four arms of CONTEST: the British government's umbrella initiative for countering extremism
It defines extremism as "vocal or active opposition to fundamental British values, including democracy, the rule of law, individual liberty and mutual respect and tolerance of different faiths and beliefs. We also include in our definition of extremism calls for the death of members of our armed forces, whether in this country or overseas."
It focuses on stopping people becoming radicalised before this opposition occurs
Millions has been spent on Prevent
It's one-on-one mentoring programme has been praised, but it's also been criticised for stigmatising Muslims and for failing to stop people joining Islamic State abroad
No one has ever formally complained against the banned Christian union and it is unclear how the group contravened Prevent policy and how long it will suspended for.
Toni Coulton from Festive told Premier's News Hour she was unaware of the specific details of why the school had taken this action but claimed the Christian Union had done nothing wrong.
"I can't imagine what a Christian union could be doing," she said.
"If one came to us and we had any suspicion that they needed some help in some way we would go to the local churches and say this CU needs some help...but we have no indication that this is the case."
It is believed to be the first Christian Union to be barred under Prevent - however there are reports that two other groups are facing similar issues.
The government has said it cannot comment on the case, as it is currently unaware which Christian union has been prohibited from meeting.
Listen to Toni Coulton speaking to Premier's Antony Bushfield.
