The Business group, which represents over 10-thousand small and medium firms, says there's huge confusion on what is expected of employers.
It says the Health and Safety Authority and public health officials are not issuing the same guidance.
Chief Executive of ISME Neil McDonnell explains the difficulties:
"The Health and Safety Authority wants employers to keep on vaccinated workers apart from vaccinated workers. On the other hand, we're told that vaccination status is a medical record, and it's subject to data protection, and it's a matter for the public health function alone, so these differences unfortunately are irreconcilable and they're causing a great deal of difficulty."