The province's Health Department says Health Canada found certain elements of the program to be non-compliant with national guidelines.
In one case, necessary information about a donor with tattoos was not obtained, but the mistake was caught in time and the recipient was fine, the department said Wednesday.
"We are taking steps to put the necessary quality assurance procedures in place so that the program can be compliant with the national guidelines as soon as possible," Health Minister Madeleine Dube said in a statement.
The department says it has suspended the program until it has interim measures in place.
Organs referred from New Brunswick will be flagged to notify the physician and recipient of the program's non-compliant status.
The department says it believes they will have the necessary measures in place to satisfy Health Canada by the fall.
The living donor program as well as the tissue program and eye bank, which are handled separately, will continue to operate.