Norton N. Bonaparte told CNN that it would be "better for us to have a separation" because it will be hard for Bill Lee to return to the department.
Earlier this week Sanford city commissioners voted 3-2 against accepting Lee's resignation and providing him with a severance package.
Lee has been on paid leave since March 22 when commissioners expressed a lack of confidence in the investigation into the Feb. 26 shooting death of Martin, 17, by neighborhood watch volunteer George Zimmerman, who has since been charged with second-degree murder by a special prosecutor.
The two commissioners who voted against accepting Lee's resignation questioned the fairness of dismissing him.
"Basically, what the city commission said is that they want to have more information," Bonaparte said. "In particular, they want to have the results of an independent investigation that would determine what actually took place that night and how the Sanford Police Department acted."
In the meantime, Capt. Darren Scott will continue to serve as acting chief of the Sanford Police Department.