A method of cleaning a membrane in a membrane separation activated-sludge process. By the method, deposits adherent to the surface of a membrane used in a membrane separation activated-sludge process can be effectively scratched off and the membrane filtration rate can be prevented from decreasing. Membrane-cleaning particles (4) in which the surface to be in contact with the water to be treated has been hydrophilized and has a surface roughness of 100-2,500 .mu.m are introduced into a bioreactor (1). The particles are caused to flow by the lifting effect of air bubbles ejected from an aerator (3) or by the fluidizing effect of a fluidizing means to thereby cause the particles to scratch off deposits adherent to the surface of a separation membrane element (2). In one embodiment, membrane-cleaning particles (4) which are non-porous or have closed cells are used. In another embodiment, membrane-cleaning particles (4) having an antibacterial ingredient, such as copper or silver, supported on the surface or in inner parts thereof are used. In a still another embodiment, the membrane-cleaning particles (4) are periodically brought into an anaerobic condition to remove microorganisms from the particle surface.