A filter cleaning apparatus used in a reaction system including; a reaction tank having a filter, first feed line connected to the filter at one end, a recovery tank connected to the other end of the first feed line, and second feed line connected to the recovery tank at one end, is provided. The filter cleaning apparatus includes; first return line connected the second feed line at one end, first and second reverse cleaning solution tanks connected to the first return line, a first flow rate adjusting valve that can adjust filtered fluid to be supplied to the first reverse cleaning solution tank, a second flow rate adjusting valve that can adjust filtered fluid to be supplied to the second reverse cleaning solution tank, and a switching section that carries either one of the filtered fluids accommodated in these reverse cleaning solution tanks by switching.