The state planning tribunal ruled on Wednesday that developer Obiter Investments, which owns a site on Flemington Road opposite the Parkville hospital, needed to change its proposal – even though two-thirds of the apartments have already been sold off the plan.

The proposed 15-level apartment tower was approved by Melbourne City Council without proper consideration of the crucial chopper flight paths. After Wednesday's ruling, the tower can now only rise to 12 levels.

Melbourne City Council's chief executive officer at the time, Ben Rimmer, apologised to the health department last year, over the council's failure to consider helicopter flight paths when approving the $40 million tower. The proposed apartment tower is 160 metres from the hospital.

State planning tribunal members Helen Gibson and Anthony Liston found that the Royal Melbourne Hospital needed 24-hour unrestricted access to the helipad.

They wrote in their ruling that, if the building were  not lowered by at least three levels, chopper pilots may "refuse to use the helipad" and "potentially [lead to] the complete closure of the helipad or permanent restrictions on night-time departures".

While it would still be possible for choppers to land on the helipad if the tower were built to 15 levels, some pilots might refuse to fly there, the tribunal members ruled.

Because the Royal Melbourne Hospital was one of the state's two recognised trauma centres, it was crucial the helipad was as accessible as possible, the tribunal found. There were 269 emergency landings last year at the hospital.

Obiter Investment could not be contacted for comment about the project.

Planning Minister Richard Wynne, responding to the decision for the government, said Royal Melbourne Hospital's emergency facilities were too important to put at risk.

He said chopper flight paths had been protected at hospitals since the original application for the apartment tower was made. The developer applied for the apartment tower in July 2014, two years before the state government brought in its flight path laws.

Helicopters have had to be diverted away from the Royal Melbourne Hospital in the past – because of cranes protruding into surrounding airspace. Emergency helicopters need straight flight paths that avoid curves that can disrupt patients and staff caring for them.

A Melbourne City Council spokeswoman said the council was "considering the decision handed down by VCAT this morning and does not intend to comment at this stage".

Two-thirds of the apartments in The Principal had been sold off the plan before the legal mess became public in June. One legal source close to the project speculated that the state planning tribunal decision could ultimately end up being challenged in the Supreme Court.