Pandya, when fit and in form, is India's preferred seam-bowling allrounder and has also been retained as vice-captain of the Rohit Sharma-led squad for the T20 showpiece co-hosted by the United States and West Indies.
Returning from an ankle injury suffered during the 50-overs World Cup last year, the 30-year-old has struggled with bat and ball in the Indian Premier League.
Under his captaincy, five-times champions Mumbai Indians have slipped to ninth place in the 10-team league and will need a miracle to make the playoff.
"The good part is he's got through all the games for MI and we've got another month and a little bit until we play our first game," Agarkar told reporters in Mumbai.
"As long as he stays fit, we know what he brings, how much balance he gives the team.
"I don't think there's a replacement for the things that he can do as a cricketer, especially with the ball. He really gives Rohit the option to play different combinations.
"So his fitness for us is critical and so far, fortunately, he's gone okay in this IPL."
Unlike Pandya, Kohli has been consistent in the IPL with 500 runs so far this season and only Ruturaj Gaikwad (509) has scored more runs than the former India captain.
Many find Kohli's strike rate of 147.59 not impressive enough but Agarkar and Rohit laughed off that criticism.
"He's been in great form in the IPL, no concerns there at all," Agarkar said stressing the need for experience in a World Cup campaign.
"You've got to prepare knowing there's a gap (between the IPL and a World Cup). That's where experience does matter a lot."
"There's no point over-thinking it."
While the IPL provides a glimpse into the form and fitness of the players, Agarkar said performance in the league alone did not influence team selection.
With the ball likely to turn in West Indies, India have picked two specialist spinners -- Kuldeep Yadav and Yuzvendra Chahal -- along with spin-bowling allrounders Ravindra Jadeja and Axar Patel.
"I wanted four spinners, three specialist seamers and Hardik as the fourth one," Rohit said.
"Based on the combination of our opponents, there's a good chance that Kuldeep and Chahal will play together..."
Inaugural champions India will begin their campaign against Ireland in New York on June 5 and also face arch-rivals Pakistan, the United States and Canada in Group A.
