John Clark left his job Wednesday after federal agents showed Cockrel a videotape of Clark accepting money this year, the Detroit Free Press reported Sunday.
Cockrel acknowledged Saturday that Clark resigned, but would not elaborate. Clark worked for Cockrel for about eight years.
The newspaper said Cockrel met with FBI agents for about 90 minutes Wednesday and viewed hidden camera footage of Clark allegedly accepting money from someone.
Federal authorities are investigating a sludge recycling contract with Synagro Technologies of Houston that the Detroit City Council approved last fall.
Conyers was among the five members who approved the controversial deal, which allowed a recycling plant to be built in Detroit and resulted in the privatization of about 140 city jobs.
Under the agreement, the city would pay Synagro about $47 million a year to handle 183,000 tons of wastewater treatment sludge.
The company would recycle some of the sludge into fertilizer and invest about $125 million in a new plant to incinerate the rest.