Atapattu's resignation comes after the island nation lost back to back Test series against continental neighbours Pakistan and India in last three months.
It has been learnt that Atapattu's resignation has been accepted by the Sri Lanka Cricket's interim chief Sidath Wettimuny.
Atapattu, one of Sri Lanka's batting mainstay during his playing days, had held the position of chief coach from September 2014 after Paul Farbrace took over as England's assistant coach.
According to reports, SLC is likely to approach former Sri Lanka batsman Chandika Hathurusinghe for the post of chief coach as he has done remarkably well with the Bangladesh national side.
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Apart from guiding them to the quarter-final of the ICC Cricket World Cup, the Bangladesh team beat Pakistan, India and South Africa in three successive ODI series.
The other name that is doing rounds is of Graham Ford.