Mr Scapens said after yesterday's meeting that he was not happy with the council's decision but that it was good to move on.
The council's decision meant that Mr Scapens will not have to go through a publicly notified Bay of Plenty Regional Council resource consent process to make the glass box a permanent fixture of the waterfront.
The process could have cost him up to $140,000.
It has been 10 months since the city council agreed to grant a new lease allowing the Landing Pontoon to operate as a stand-alone glass box, but it had to be open and operating by September 30 this year.
Mr Scapens was yesterday unable to give the council a new date of when it would be operating, saying he could not give an assurance he would get consent from the regional council.
However he thought that the summer of 2013-14 would be a logical timeframe.
Councillor Catherine Stewart said she had received a lot of feedback that the waterfront looked better without the glass box _ it had a better ambience.
"It is time we moved on.''
She said the glass box was there by default and the council had been surprised when it turned up with the Kestrel.
Councillor Larry Baldock wanted to give Mr Scapens until September next year because the council stood to lose revenue by not allowing the glass box pontoon to stay on the waterfront.
It provided a useful facility for the southern end of the waterfront, and the other side of the pontoon would have been a landing for services like jet boat excursions.
Councillor David Stewart said the description of a glass box was apt.
"Many of us were surprised when it turned up alongside the Kestrel.''
Councillor Wayne Moultrie said: "We have a waterfront that looks good _ we don't need to denigrate what we have got by the return of that dreadful glass box . . . we want a waterfront clear of clutter.''