The proposed bridge would connect Alice and Edward streets and Scott Street or Thornton Street.
Lord mayor Adrian Schrinner had previously announced plans for a $190 million cycling and pedestrian bridge to span that section of the Brisbane River.
He said the size of superyachts would require the bridge to be built higher than the Captain Cook Bridge,which would increase its footprint and make construction more expensive.
State Development Minister Cameron Dick said if the proposed bridge blocked yachts from cruising down the river,it would need to be redesigned.
"We want the $600 million superyacht industry to access as many parts of Brisbane as possible,to boost tourism and jobs for Queenslanders,"he said.
A pedestrian bridge has been proposed at Kangaroo Point.Credit:Richard Kirk Architect
"This has been raised with Brisbane City Council and we understand there have been constructive discussions between council and the department."
Cr Schrinner on Wednesday said the council had repeatedly expressed reservations about the potential for a superyacht berth at Kangaroo Point and he believed there were better locations.