New Zealand reached the final of this month's Champions Trophy in South Africa but domestic media has reported that unnamed senior players wanted Moles removed and New Zealand Cricket's review had been critical of Moles' performance.
"Andy Moles has resigned as coach of the Blackcaps in the best interests of New Zealand cricket," NZC said in a statement.
"This follows a review of the Blackcaps performance upon their return from Sri Lanka and the Champions Trophy.
"The parties reached an amicable agreement at mediation on Friday, the terms of which are confidential to the parties," the statement said.
Moles, 48, succeeded John Bracewell, last year as New Zealand coach, and was contracted until the 2011 one-day World Cup.
"Andy has made a significant contribution to cricket in New Zealand including the recent success on the Blackcaps team in making the final of the Champions Trophy," NZC chief Justin Vaughan said.
No head coach would be named for the ODI series against Pakistan in the United Arab Emirates next month, the statement said.
"It has been a great privilege to have been the coach of the Blackcaps and, while I am sad to be leaving, I wish the team every success in the future," Moles said.
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