The Australian, who had a failure of the system on his RB7 at the start of the Malaysian Grand Prix last week, had more problems on Saturday in the final practice session before Shanghai qualifying.
"We are doing our best to make sure KERS is in working order on Mark's car but it's very tough," team boss Christian Horner told the BBC shortly before qualifying.
"It's probable we won't run KERS in qualifying on Mark's car but we will in the race. Sebastian (Vettel) will run KERS throughout," he confirmed.
Vettel won both the Australian and Malaysian grands prix from pole.