"I am not comfortable with the idea of Modi," Patnaik said while participating at an interaction programme here.
Disagreeing with the idea that the next polls will turn into an presidential form of election between Modi and Rahul Gandhi, Patnaik said that both of them do not have "pulling power."
The next elections will be fought on the basis of ideologies rather than personalities, Patnaik pointed out.
Earlier, after Modi being named as the chairman of the BJP's national election campaign committees, Patnaik had said that both Modi and Rahul Gandi lacked pan-India acceptance.
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Patnaik's statement on Modi virtually rejected senior Congress leader and Union Minister Srikant Jena who last week alleged that the BJD president harboured secret understanding with his Gujarat counterpart.
Patnaik, who earlier in the day claimed that his party was equidistant from both the Congress and BJP, said that he would rather prefer a third front as it is "healthy" for the democracy.
Asked whether his party would play a vital role in the formation of government at the centre after 2014 elections, Patnaik said: "Let the numbers come and results of 2014 elections come out.