Hull are second from bottom in the Premier League table, with eight games to go. They have 24 points, with Burnley topping them on goal difference.
"Hull City AFC confirms that Phil Brown has been relieved of his managerial duties at the club," read a statement on the club's website.
"Brian Horton and Steve Parkin will take charge of first-team duties until further notice.
"We would like to place on record our sincere thanks to Phil for the major success achieved during a period of four seasons in charge at the club."
Brown took a gamble on Zaki in January, hoping the Egyptian international striker could score a few goals and help the club beat the drop.
However, Zaki, on loan from Zamalek, started just twice and failed to find the net.
Brown has been in charge of the team for the last four years. He guided Hull City to promotion to the Premier League for the first time in their history in 2008.
According to the Times, veteran manager Alan Curbishley and former Middlesbrough coach Gareth Southgate are favorites for the vacant post.
Southgate has been coaching two other Egyptians, Mido and Mohamed Shawky, during his first managerial experience with Middlesbrough.
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