"Our door is still open for Whatmore. He is a great coach and (the) Bangladesh team has improved a lot during his four-year tenure," Bangladesh Cricket Board (BCB) general secretary Mahbub Anam told AFP.
Anam, who heads the board's coach-hunting mission launched when Whatmore quit last month, said Bangladesh had not said goodbye to the Australian coach, noting: "He made the decision to leave the post."
The BCB had reportedly offered an improved package after Whatmore decided to seek the high-profile job of Indian coach immediately after Greg Chappell quit following India's poor show in the Caribbean World Cup.
But on Monday Indian authorities picked South African Graham Ford as frontrunner for the post and said Whatmore was out of contention.
The 53-year-old was an early favourite for one of the toughest coaching jobs in cricket after he publicly expressed his interest in taking on Rahul Dravid's men.
Under Whatmore, cricket minnows Bangladesh won their first Test and beat teams such as Australia, South Africa and India in one-day internationals.
The BCB this week made Australian Shaun Williams interim coach for Bangladesh's five-week tour of Sri Lanka later this month and said a new coach would be named after the tour.