The tournament has been reduced to 54 holes and the third round, which began briefly on Saturday, will be concluded on Sunday with Malaysia's Gavin Green leading on 14 under, three strokes ahead of Belgium's two-time winner Thomas Pieters, Germany's Marcel Schneider and England's Richard Mansell.
A statement from the DP World Tour read: "Due to inclement weather in the Prague area, the D+D REAL Czech Masters has been reduced to a 54-hole tournament.
"Heavy rainfall, which began on Friday evening and continued throughout Saturday, rendered areas of Albatross Golf Resort unplayable due to standing water.
"The third round, which began on Saturday morning, will now be completed on Sunday August 21 and the winner of the tournament decided after 54 holes."
David Williams, tournament director of the D+D REAL Czech Masters, said: "The continued rainfall we have experienced means that, despite the strenuous efforts of the greens staff and volunteers, there is no way the course is going to be playable for the rest of the day."