Wessells joined the club in 2003 and had plenty of initial success but the club admitted tensions had "run high" during a difficult season this year which has seen the team prop up Division Two of the county championship.
Northants chief executive Mark Tagg told BBC Sport: "He had signed a contract up until 2007 but has left the club by mutual consent.
"We will make an announcement on his successor in due course."
A statement on the Northants website read: "Kepler joined the county in 2003 and in his first season got promotion to Division One of the County Championship and the National Cricket League.
"In the years following the club has been forced to tighten its belt and reduce the size of the budget available for squad development.
"Despite this difficulty the team has maintained its Division One status in the National Cricket League and has figured prominently in the Twenty20 Cup.
"However 2006 has been a difficult season.
"A poor run of results had led to frustrations for the director of cricket, the dressing-room and the club and inevitably tensions run high in these situations.
"Kepler feels that he has now taken the club as far as he thinks possible and we have amicably parted company at this time."