BJP had demanded that Chacko take a decision on calling Prime Minister Manmohan Singh and Finance Minister P Chidambaram before JPC.
"I want them to return to committee meetings and stay till we table the report. But if they continue with their protest, JPC will meet in their absence," Chacko told PTI.
He also said any future decision will be taken collectively by JPC and he would not take a call on the issue on his own.
"I will not use discretionary powers of the Chairman. I want the members to take a call," he said.
Last week, five BJP members had stormed out of the meeting alleging their Congress counterparts had used foul language when they demanded calling Singh and Chidambaram before JPC.