When an out-of-basin type separation membrane, which is connected to a biological treatment tank through a circulation passageway for filtering tank water, is cleaned, a part or all of the backwash drainage containing the sludge peeled from the membrane surface is returned to the biological treatment tank through a backwash drain passageway or circulation passageway to maintain MLSS of the biological treatment tank constant. In the case of chemical cleaning, the sludge is peeled from the membrane surface by backwash with water, and the sludge is discharged out of the membrane module through a sludge line and then followed by chemical cleaning. Thus the need for using a large amount of a chemical solution is eliminated and the peeled sludge containing the chemical solution can be discharged out of the system as well, thereby preventing the microorganism from being damaged by the chemical solution.