The Sunset review recommends giving Governor Rick Perry the power to appoint all seven commissioners to the Port of Houston Authority.
Right now Harris County and the City of Houston each appoint two commissioners to the board and jointly select a chairman.
The City of Pasadena and smaller municipalities select the final two board members.
Houston Mayor Annise Parker says the port is the Houston region's single largest economic driver and she thinks it's under attack from state leaders.
"The city and the county are united in the belief that having the governor appoint members of the Port Commission is a mistake. It takes away local control, it takes away the ability to be engaged with those who are most impacted by the port."
The Sunset report says the Port Authority is mismanaged and needs state oversight.
The city and county are due to select a new chairman to replace Jim Edmonds, who is still serving although his term ended earlier this year.
"Chairman Edmonds serves until his successor is named, he has served ably. Lynn Waterworth, the new director over there, has done an outstanding job and has already implemented many of the suggestions in the Sunset Review. So we think the port's in good shape."
Parker wants to appoint current commissioner Janiece Longoria as chairman, but says she hasn't heard from the county on whether they agree. The legislature will have the final vote on whether to hand port commission appointments to the governor next year.