The Scot was a controversial appointment back in November, following revelations of offensive text messages sent between himself and then Cardiff City head of recruitment Iain Moody during Mackay's time in south Wales.
Since arriving at the DW Stadium, Mackay has overseen five wins in 24 league outings, none of which have come in front of Wigan's home fans.
That run leaves the club 23rd in the table, eight points adrift of 21st with just five games remaining.
"This is a very difficult decision to make but I feel that for the long term future of the club, there needs to be a change now. I wish Malky all the best for the future," said Wigan chairman David Sharpe in a statement.
Wigan's dismal situation is in stark contrast to their fortunes in recent years, having enjoyed a run of eight seasons in the Premier League, capped by 2013's memorable FA Cup triumph.
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