He was 77.
Mohapatra had been undergoing treatment at a private hospital in Mumbai. He passed away tonight, his family said.
Regarded as the chief strategist and mentor of Odisha Chief Minister Naveen Patnaik, the former IAS officer of 1963 batch played a key role in deciding the shape and contours of the Biju Janata Dal (BJD) after the regional party was formed in 1997.
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Mohapatra was the Principal Secretary to the Chief Minister when Biju Patnaik occupied the top post.
Mohapatra got himself actively involved in the affairs of the BJD before the assembly elections in 2000 and continued to play a key role in consolidation of Naveen Patnaik as the undisputed leader of the regional party.
Besides his contribution towards strengthening the BJD at the grassroots level and making it a cadre-based party, Mohapatra played a major role in the BJD's move to part ways with the BJP in the run up to the 2009 general elections.
The strategy worked and the BJD swept the polls, raising Mohapatra's stature in the party. He was Rajya Sabha member from 2010 to 2012.
However, Mohapatra was removed from the party in 2012 on charges of attempting a coup to topple the chief minister when Naveen was abroad. Subsequently, he formed Odisha Jana Morcha (OJM) and became its founder president.
OJM Secretary S P Swain said the body of Mohapatra will be brought here tomorrow for last rites.
A host of dignitaries, including Union Petroleum Minister Dharmendra Pradhan, Lok Sabha Member Baijayant Panda, Odisha BJP President Basant Panda, Odisha Pradesh Congress Committee (OPCC) President Prasad Harichandan have expressed condolences over the death of Mohapatra.
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