The Commission had last week dismissed a Congress complaint alleging that the PMO misused the NITI Aayog for gathering information on Gondia, Wardha and Latur Lok Sabha constituencies of Maharashtra ahead of Prime Minister Narendra Modi's visit.
The poll body had also cleared the PMO and NITI Aayog despite Election Commissioner Ashok Lavasa suggesting that CEO Amitabh Kant should be asked to know about whether any such information was sought.
The Commission had taken the decision as Chief Election Commissioner Sunil Arora and Election Commissioner Sushil Chandra felt the that Congress' complaint was without basis, as the exemption had been granted to the Prime Minister to combine an official and electioneering visit.
The Election Commission had sought comments from Kant on the matter earlier, but he denied any wrongdoing. Following Lavasa's dissent, the poll panel sent a second notice to Kant on Thursday. However, the NITI Aayog CEO has not been given any deadline to file a response.
Earlier this week, Lavasa recused himself from the Election Commission's meetings on deciding violations of the poll code, saying that his "minority decisions were going unrecorded". Lavasa had opposed five clearances that the poll panel gave to Modi and Bharatiya Janata Party National President Amit Shah in complaints of Model Code of Conduct violations.
However, in a statement on Saturday, Arora denied any rift in the Election Commission, claiming that news reports of a disagreement were "unsavoury".