The Ministry of Business, Innovation and Employment will bring together the existing functions of the ministries of Science and Innovation, Labour, and Department of Building and Housing.
Mr Joyce said in a statement the Government was committed to building a more competitive and productive economy that would grow more and bigger businesses.
"Our business growth agenda will make it easier for businesses and companies to access innovative ideas, markets, capital, skilled workers, resources and the supporting public infrastructure."
The Public Service Association said the new ministry would look to save millions of dollars on administrative and policy functions but risk losing valuable employees and damaging morale.
Mr Joyce said the rough indication was between 50 and 55 people would lose jobs. In addition, 84 vacant positions across the agencies would not be filled.
The Government had previously said it expects the ministry to deliver savings through the consolidation of corporate services of about $5 million to $6 million a year, and of policy capability of about $2 million to $5 million a year.
PSA national secretary Brenda Pilott said the PSA had always been concerned the creation of a super-ministry was in part motivated by cost-cutting. The Government's announcement confirmed those fears.
The cuts to policy staff appeared "particularly misguided", she said.
"The Government has said it wants to strengthen the public sector's ability to think strategically across issues. Instead, it seems to be cutting staff numbers based on a one-size-fits-all model that says all departments should have the same proportion of policy staff - even though the needs of each department will be different."
The projected long and unsettling merger process, which the Government said could take two years, risked losing experienced employees who were assets to the Government.
That risked creating so much disruption that staff could no longer deliver public services effectively, Ms Pilott said.
State Services Minister Jonathan Coleman said it was envisaged the existing separate agencies would form the initial functional units of the new ministry, which would then be further consolidated over time.
For most workers, the transition would be seamless. They would be doing the same job with the same pay and conditions on July 1.
