Modi, who was accompanied by priests and local BJP leaders, spent more than 30 minutes inside the temple and entered the sanctum sanctorum to seek blessings of the Lord.
"This is the first visit of Modi to the temple after becoming Prime Minister. Earlier before the 2014 general elections, Modi had vowed to come here again if his desires are fulfilled. As he has become prime minister, Modi came to express his gratitude to the Lord," said a priest accompanying him.
While returning from the temple, Modi, who was attired in an off white kurta with yellow 'Anga Vastram' on his shoulder, waved at people lined all along the Grand Road in front of the Temple.
"Touched by people's warmth and affection in Puri," Modi tweeted after having a darshan of the trinity - Lord Balabhadra, Devi Subhadra and Lord Jagannath.
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The Odisha Police made elaborate security arrangements by deploying more than 250 personnel for the Prime Minister's visit.
The security personnel were also deployed on roof tops of buildings on both side of the Grand Road in front of the Temple.
The Shree Jagannath Temple Administration (SJTA) had vacated the temple for the VIP visit.