MSF, the largest trade union in Enterprise Ireland, claims the agency intends to stop offering technical services to companies.
About a dozen MSF staff are in dispute with the new agency over a decision to close its geotechnical division which provides a quality control service to construction companies.
The union claims the closure is the "tip of the iceberg" and a political decision has been made that technical services will not be part of the new agency's remit.
Enterprise Ireland says the geotechnical service is being closed because there are enough private sector companies offering it. A spokeswoman said no decision has been made about what technical services will be provided in the future.
The geotechnical staff have worked on projects like the Intel Fab 14 facility in Leixlip, Co Kildare, the Masonite plant in Co Leitrim, the Hewlett Packard plant in Celbridge, Co Kildare and the Lee Tunnel in Cork.
The staff advise companies on the correct materials to use in construction and whether the location where building is taking place is safe.
The dispute centres on whether staff are to be re-deployed to other areas. MSF says some staff do not want to be re-deployed to jobs for which they have no training.
