Up to 80 students from Ireland fear they have each lost over €80,000 in fees, which they paid for flight training in the US.
The Irish Aviation Authority has suspended the training licence of the Waterford-based Pilot Training Centre of Ireland.
The trainee pilots are stranded in Florida after being told that their course will not be continuing.
The trainees had paid fees to the Pilot Training Centre of Ireland (PTC), but the Florida Institute of Technology Aviation (FIT) told students that they would not be allowed into the air again.
In a statement, PTC confirmed it had terminated its contract with FIT, following what PTC said was the Florida institute's "non-performance".
It said some, but not all of the students in Florida will lose money as it has already paid for services that FIT has not yet delivered on.
PTC Executive Chairman Mike Edgeworth said: "We regret very, very much what has happened and we apologise fully to all our students.
"We have been trading very successfully for ten years and our current problems are due to issues that are beyond our control".
Mr Edgeworth said 39 students who have recently enrolled in PTC should not be financially impacted and for 25 people who recently started training, he said the financial impact "should be minimal".
One trainee pilot told RTÉ's News at One that if he does not get the money back from the course, it will leave his family $100,000 in debt.
Daniel McLernon said: "We've basically been sitting around since then doing nothing. We've been told absolutely nothing.”
The IAA has said in a statement it is aware of certain difficulties with the Florida Pilot Training College.
An IAA officer is in Florida to brief the students and to explore the possibility of allowing the students to continue their training in Florida or back in Ireland.
The mother of one 19-year-old trainee pilot told RTÉ News that they had noticed problems with the course at an early stage.
She said her son, who does not wish to be identified, began the course in November of last year and it was 12 weeks before he was given his first flying lesson.
She also said her son and other students are due to be evicted from FIT accommodation on 15 July.
Another trainee told RTÉ News that their visas are due to expire on 17 July.
It is understood that the students paid €84,875 in fees in four instalments into an account in Dublin, and from there the money was to be transferred to the FIT.
PTC said it has entered into commercial negotiations with FIT to resolve the problem and that a number of students from Air Astana have already transferred from PTC to FIT.
It said all students will be accommodated in Florida until 15 July and their visas will remain valid until 17 July.
PTC also said the cohort of students who are due to finalise their training in Waterford will complete that training.
The students said a FIT representative told them that it had not received two payments due.