Hospital services will increasingly be organised in groups or "clusters" with their own overall governance and management structures, the Prospectus report has predicted.
It said this, combined with the need to reconfigure existing hospital roles, would present "challenging difficulties".
However, the manner in which hospital services are configured will not be unveiled until a separate report on medical staffing in the health service - the so-called Hanly report - is published next month.
The Prospectus report said a National Hospitals Office (NHO) should now be set up to oversee the day-to-day running of all publicly-funded hospitals.
It will focus on reducing waiting lists, managing the current activities of the National Treatment Purchase Fund, approving consultant posts in publicly funded hospitals, ensuring hospital services are integrated within the wider health system, managing the interface with private acute providers, ensuring delivery on national health strategy targets and relieving pressures on A&E services.
Its role will also be to "bring clarity" to the function of many of the State's hospitals.
"We recognise that many major hospitals play multiple roles: local, regional, supra-regional and national (in some cases).
"Part of the NHOs remit will be to bring clarity to these distinctions and have this reflected in regional planning and operations," the report said.
It added: "We anticipate that hospital services will increasingly be organised in hospital groups or clusters with their own overall governance and management structures, where this is not already the case.
"At regional level, the NHO will have a role in putting those groups in place and ensuring they operate effectively. This will require different approaches depending on the region involved.
"In the eastern region the existence of major academic teaching hospitals with a range of specialty roles alongside a number of stand-alone specialist hospitals, some of which also have national specialty status, presents a complex set of policy, organisational and managerial challenges.
"Elsewhere in the country, the need to reconfigure existing hospital roles, to meet local and regional demands, or to align with best practice in treatment and professional training presents other equally challenging difficulties," the Prospectus report said.
Prospectus has recommended that all funding (capital and revenue) for acute hospital services be allocated through the NHO and that publicly funded hospitals should have employing authority in their own right.