The Latics hired the former Arsenal, Manchester City and Liverpool defender following Leam Richardson's dismissal as they sat 22nd in the Championship.
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However, they have since sunk to the bottom of the table and gone winless in nine matches under Toure.
In a statement, Wigan CEO Malachy Brannigan said: "Firstly, I'd like to thank Kolo, along with Kevin [Betsy] and Ash [Johal], for their efforts during their time at the Football Club.
"Unfortunately, the results on the field have not been as we would have liked and as tough a decision as this was, the board felt it necessary to give us the best possible chance of remaining a Championship club next season.
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"We know that this time of year is a key period for any football club, ourselves included.
"Therefore, we will now work swiftly and effectively to ensure the right person is appointed as the next permanent manager of Wigan Athletic, with the immediate objective of remaining in the Second Tier for next season."
After a draw and a loss in his first two games, Toure and Wigan were beaten 4-1 in three consecutive matches.
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Two more draws would follow before another two defeats, with Wigan now searching for their third manager of the season.
talkSPORT understands that former Hibernian boss Shaun Maloney is in contention to replace Toure.
He has also worked as part of the coaching staff for the Belgium national team and used to play for Wigan, Celtic and Aston Villa.
Wigan are four points off safety and are joined in the relegation zone by Huddersfield Town and Blackpool.
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