Anil Kumble on Tuesday stepped down as India's head coach saying the Indian cricket board had informed him that captain Virat Kohli had reservations about his 'style'.
Kumble's decision to quit came after a rift between him and Kohli, with the the Board of Control for Cricket in India (BCCI) advertising the coach's job before the Champions Trophy.
The BCCI had urged Kumble to carry on as coach until the end of a West Indies tour starting June 23, but the former India captain did not travel with the team that left from England on Tuesday.
"The Board of Control for Cricket in India (BCCI) confirms that Mr Anil Kumble has withdrawn his services as the post of the Head Coach for the Senior India Men's team," said a board statement.
"While the Cricket Advisory Committee had endorsed an extension to his tenure as Head Coach, Mr Anil Kumble has decided not to continue as the coach," the statement added.
In his resignation letter, Kumble said his partnership with the captain was "untenable".
"I was informed for the first time yesterday by the BCCI that the captain had reservations with my style and about my continuing as the head coach," Kumble wrote in the letter, which he tweeted on Tuesday.
"I was surprised since I had always respected the role boundaries between the captain and coach," he added.
The BCCI had denied any rift in the Indian camp, but Kumble's letter confirmed media reports that board officials had tried to resolve the spat.
"Though the BCCI attempted to resolve the misunderstandings between the captain and me, it was apparent that the partnership was untenable and therefore I believe it is best for me to move on," the former captain wrote.
Kumble's resignation came two days after India's 180-run loss to Pakistan in the Champions Trophy final.
However, India board officials praised 46-year-old Kumble, who was put in charge of coaching last June, for his tenure.
"We wish to place on record our sincere appreciation for the immense contribution by Anil Kumble to the team which enabled India to attain the No.1 Test position," acting BCCI secretary Amitabh Choudhary said.
"Indian cricket needs his continued contribution in various capacities and wishes him all the best in his future endeavour."
The BCCI has retained the rest of its coaching staff for the West Indies series, with MV Sridhar supervising the team's management.
India will play five one-day internationals in the Caribbean, with a Twenty20 international wrapping up the trip on July 9.