Youth With a Mission England was told on December 23rd that it's licence to sponsor visas which allowed it to help missionaries come to the UK had been suspended.
It was after an inspection by the UK Visas and Immigration office found clerical issues with its administration process.
YWAM is able to bring missionaries and their families to the UK currently but if it can't resolve the problems within 20 working days that privilege would be removed.
If this happens, the 350 missionary families volunteering for YWAM in the UK, half of the current workforce, will have 60 days to leave the country.
YWAM said it would "inevitably mean shutting down" some of the training and service opportunities in the UK.
"While we recognise and support the UKVI's legitimate right to concern over compliance to the rules, we do not feel that the issues raised in the letter from the UKVI justify such a draconian outcome as losing our licence would produce," the charity said.
"We are cautiously hopeful that through dialogue and by demonstrating our determination to follow the regulations as carefully as possible they will allow us to continue our operations in the UK as part of a global charitable faith-based movement.
"We recognise that YWAM has never been the type of organisation which fits neatly into boxes. Nonetheless, we are doing everything we can to comply with the law and ensure that our missionaries remain a blessing to the UK and, through our YWAM England and Wales teams, to the rest of the world that YWAM seeks to share the love of Christ with."
The Evangelical Alliance, which the charity is a member of, is now asking for prayer for a "favourable resolution" to the inquiry and is urging supporters to write to their MP before 20 January 2015, when the final decision will be made.
A Home Office spokesperson said: "We continually and routinely monitor all licensed sponsors. Where we find evidence that sponsors are not fulfilling their duties we will suspend or remove their licence."