The grand Grade B listed building was attacked by arsons three times over the weekend, causing more damage to the building, which was gutted in a blaze last March.
Mr Gilligan, who bought the site in 2006 for a nominal fee of £1, said grant aid to provide hospitality and leisure facilities at the former courthouse was not sufficient.
One city councillor has suggested the historic site should be vested by the Department of Social Development (DSD).
Ulster Unionist Stephen Nicholl said the courthouse and the adjacent Gaol, along with Girdwood, were supposed to represent the future of north Belfast in terms of economic and educational development.
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"Instead after the usual Masterplan exercise we have the usual inaction and failure to deliver for people in the most deprived area of Northern Ireland," claimed Councillor Nicholl.
"All across Belfast buildings carry the signs showing they have been vested by DSD, surely this facility should be a priority and given that no more should be paid for it than it was sold for the Department could move quickly," he added.
Mr Gilligan said he is prepared to "work with anyone" in order to secure the future of the courthouse plans.
"Both of those schemes have made it clear from the outset that they require significant grant aid - the level of grant aid, particularly for the hotel is not forthcoming," he said.
"So in one sense it is back to the drawing board and it is back to finding some form of innovative use for this building which requires a lesser amount of grant aid.
The developer, who also chairs the Northern Ireland Policing Board, said public funding hasn't matched his expectations
Crumlin Road courthouse's ornate style was the brainchild of renowned architect Sir Charles Lanyon, who also designed City Hall, Custom House, Queen's University.
(PR/BMcc)
