Omar, whose National Conference (NC) is a part of the UPA, said his father, Union minister Farooq Abdullah, also felt the same way about the announcement.
"Was talking to my dad last night and he felt the same way — setting up a commission of inquiry in the dying hours of UPA 2 is just wrong," Omar twitted.
The chief minister said the decision should have been implemented when it was taken in December.
"If the decision to appoint a commission was taken in December, it should have been implemented. To appoint a judge 5 months later is wrong," he said.
On Friday, the central government had said a judicial commission to probe "snoopgate" allegedly involving Modi will be in place before the Lok Sabha poll process comes to an end on May 16.
The UPA government had decided four months back to set up the inquiry commission but the process got delayed reportedly because of its inability to find a judge, who was ready to take the task.
The Union Cabinet had announced that the commission, to be headed by a retired Supreme Court judge or a retired Chief Justice of a high court, will also look into charges of snooping on Himachal Pradesh chief minister Virbhadra Singh by the previous BJP government when he was in the opposition as well as the leaking of the call data records (CDR) of Jaitley in Delhi.