Henderson isn't sure what caused the setback after he threw two pain-free bullpen sessions.
"Just frustrating," Henderson said. "I've still got my head up and hopefully I'll be back for this season at some point."
The plan had been for the right-hander to make three appearances for Huntsville and rejoin the team. Now, there is no timetable for his return.
"We were hoping for two or three outings and he'd be back with us," manager Ron Roenicke said. "That's not the case."
Henderson went 5-5 with a 2.70 ERA and 28 saves for the Brewers last season. He entered Spring Training as the team's closer, but when his velocity dipped, the team turned to Francisco Rodriguez as their closer.