Rajya Sabha chairman Hamid Ansari and the BJP disagreed with each other on the day-long disruption on the I-T department's notice to the Gujarat government.
An angry Ansari expressed strong disapproval of the repeated adjournments when the House met after lunch.
He described the ruckus created by BJP members as "an extraordinary commentary on the functioning of the Indian democracy".
Earlier, as soon as the House assembled, the BJP MPs were on their feet demanding a statement from finance minister Pranab Mukerjee over the I-T inquiry into MoUs signed by the state government during the Vibrant Gujarat summit.
Taking strong exception to Ansari's remarks, Jaitley said, "Now we are told that asking for this imbalance in federalism not to be created in this manner is an extraordinary commentary on the functioning of Indian democracy.
"If we are to be strictured by the Chair in this manner, how do we expect that the proceedings of the House will go on."
Jaitley said the BJP wanted a response from Mukherjee and if he was unavailable, some other minister could assure that I-T actions would be withdrawn.
"It's an unprecedented thing. We expect a positive response from the central government so that the proceedings can go on," he said.