Cr Terry Molloy suggested the centre could be built between the proposed extension of Tauranga Marina at northern side of the recreation reserve and a new boat ramp and trailer boat park at the southern end.
Cr Bill Grainger said there was plenty of room for all on the reserve.
''I think it will be great.''
Mayor Greg Brownless said the move was a step forward.
''But don't pop your Champagne corks yet, there is still a process to go through.''
The decision by the full council followed a committee meeting last month which required the casting vote of chairman Max Mason to keep the land next to the fishing club in contention.
Mason and Steve Morris were the only councillors to support the staff recommendation to stick with the area neighbouring the club.
Morris was concerned a switch to Marine Park was planning by default.
''We need to take a long-term strategic look at the entire area because it was some of our best seaward-facing land.''
Morris said the council needed to do what was right for the whole community. The marine research station should be allowed to go ahead but in terms of the next resolution, the council was planning by default.
''The wider public will miss out.''
Council staff also cautioned against Marine Park, saying the land satisfied fewer development requirements. It was subject to the Reserves Act and had development issues.
The council was also removing a feasible open space from consideration before the Marine Park land had been assessed, and extended the timeframe before the university had certainty on a preferred site.
As the council stood to take a short break in order to draft a replacement recommendation, a councillor was heard to utter a reference to it becoming another museum issue.
When debate resumed, Mason said the university development went to the heart of what Tauranga was about - a safe harbour.
''It goes to future of who we are and our economy.''
Cr Kelvin Clout said the marine research station would bring massive benefits and some unexpected cultural and social advantages. The council had taken a long and considered view and he disagreed they were planning by default.
Cr John Robson said the council did not need to hang so much on the project in order to get it across the line.
''It is not our saviour and it will not transform the city.''