"Fitness was a clear challenge and we wanted someone who was likely to be available more often," Agarkar said during the joint press conference.
"He is one of the best T20 batters and as captain, he is likely to play all the games. We think he is a deserving captain and we will see how he fits into the role."
Regarding star all-rounder Pandya, Agarkar said, "Hardik's skill-sets are difficult to find and fitness is difficult to find. we have got a bit more time and we can look at a few things.
"Fitness was a clear challenge and we wanted someone who was likely to be available more often," Agarkar said.
"We have taken general feedback from the dressing room also," he added.
As regards to former vice-captain KL Rahul being overlooked, he retorted, "I wasn't there when KL was superseded."
The T20 series against Sri Lanka will start on July 27, followed by games on July 28 and 30.
All the matches will be played at the Pallekele International Cricket Stadium.
Suryakumar Yadav will lead a 15-member T20 squad in the three matches.
After that, the ODIs will be held on August 2, 4 and 7 at the R Premadasa Stadium in Colombo.
Rohit Sharma, who retired from T20 internationals after leading India to the World Cup triumph in the West Indies last month, will return as the skipper of the one-day international team.
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