Roy has submitted several complaints to Returning Officer Mohan Gandhi of booth capturing, intimidation of voters and polling agents, lack of security and lack of deployment of central paramilitary forces in the north Bengal constituency.
The complaints were conveyed to the EC, who then sought the report, election office sources said.
Roy also threatened a sit-in in front of the district magistrate's office alleging polling in Cooch Behar was not free and fair, but withdrew the programme after the EC order.
The party's sources claimed that TMC men drove away voters waiting in queues outside polling stations at Bamanhat and Kalmati in Dinhata.
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CPI-M, in a complaint to the election office, alleged a party worker was wounded in an attack by TMC at Shikarpur area of Mathabhanga.
The two sides also clashed at Sitalkuchi after Left parties protested against alleged false voting and one Left Front polling agent was injured in yet another clash at Andaran Fulbari in Tufanganj under Alipurduar constituency, the party alleged.
Congress candidate, Keshab Roy criticised the ruling Trinamool Congress in the state and said the administration failed to deploy the para-military forces and none were seen in Cooch Behar town.
TMC candidate, Renuka Sinha brushing aside the allegations said the opposition parties had failed to post election agents at many places and so the question of forcing them out was baseless.
Meanwhile, the polling in Coochbehar constituency till 2 pm was 55.86 per cent, according to EC sources.