Chief Election Commissioner Mahinda Deshapriya said he has received complaints that troops were being deployed in the northern Wanni region in violation of the election laws.
"I have already taken this up with the army commander, who says he has not ordered troops to deploy," Deshapriya told reporters on the eve of the election.
"I have been told that there had been 'stand-by orders' given to send the army to police stations and other vital institutions," he said.
Rajapaksa is also criticised in these areas because of the tardy reconcilitaion and rehabilitaion process and war crimes allegation against the Sri Lankan troops during the nearly three-decade war.
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The Tamils, who make up the largest minority in Sri Lanka, could be the deciders as the majority Sinhalese, who account for 70 per cent of its 21 million population, appear likely to be evenly distributed between Rajapaksa and his arch rival Maithripala Sirisena.
The broadcasters were told they would be taken off the list of media houses allowed to broadcast election results if they continue to violate election laws.
Meanwhile, the High Court today refused to vacate a District Court order barring the Independent Television Network (ITN), Rupavahini, Swarnavahini and Derana from broadcasting election campaign propaganda.
Deshapriya said troops had no role in the polls and police were capable of esuring free and fair polling at 49 counting centres and 12,314 polling booths, at which 15 million people are eligible to vote.