Former West Indies head coach Phil Simmons will take charge on an interim basis until next year's Champions Trophy.
"Hathurusingha has two counts of misconduct," Bangladesh Cricket Board (BCB) president Faruque Ahmed told ESPNCricinfo on Tuesday.
"First is about an assault on a player. Secondly, he took too many leaves, more than what was in his contract."
Sri Lankan Hathurusingha, who coached Bangladesh from 2014-2017, returned for his second stint in January last year but Ahmed questioned BCB's decision to re-appoint the 56-year-old.
Ahmed took charge of the BCB in August following Nazmul Hasan Papon's resignation amid political upheaval in the country and said Hathurusingha should not continue as head coach.
Under Hathurusingha, Bangladesh failed to get past the group stage in the last two white-ball World Cups but registered a historic 2-0 Test series win over Pakistan in September -- their first overseas series victory in the format in 15 years.
However, India then whitewashed Bangladesh at home in a two-match Test series and secured a clean sweep against captain Najmul Hossain Shanto's side in a three-match Twenty20 international series last week.
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