The party alleged this in a memorandum submitted to Chief Election Commissioner VS Sampath, who is on a visit with his full team to Gujarat where Assembly polls will be held on December 13 and 17.
Speaking to reporters later, state Congress President Arjun Modhvadia said officers of the State Government are still taking orders from the Chief Minister.
Administration of a state is controlled and supervised by the EC once elections are announced. But in Gujarat, administration is still being run from the Chief Minister's Office, Modhvadia said.
Congress alleged in the memorandum the Chief Minister is using Government machinery for communal polarisation ahead of the election. The party asked the EC to remove BJP "sympathisers" from poll duty and transfer all officers who have completed three years in their present posts.
Congress said traders and businessmen should not be harassed over movement of cash. Modhvadia raised question over the funding of NaMo Gujarat TV channel, run by BJP.
Meanwhile, Sampath along with Election Commissioners H S Brahma and Nasim Zaidi, and senior Government officials reviewed poll preparedness.
BJP, in its representation to the EC, raised the issue of poll panel's rule to seize more than Rs 2.5 lakh cash in transit. The ruling party demanded that the EC relax this rule till the end of Diwali.
"The BJP raised the issue of releasing irrigation water for agriculture crop which has been stopped by the EC," party leader Amit Shah said. "We also raised the issue of poll code violation by cleric Maulana Vastanvi for his speech at Mandvi," he said.
Representatives of other political parties like NCP, BSP, CPI and CPI(M) also met the EC team and gave their suggestions for better conduct of polls.