Remova os espaços do arquivo CSV:
sth,sth,"100,000,000",sth,"200,000"
sth,sth,"200,000,000",sth,"500,000"
E tente usar esta instrução para carregar dados -
LOAD DATA INFILE 'thefile.csv' INTO TABLE mytable
FIELDS TERMINATED BY ',' OPTIONALLY ENCLOSED BY '"'
LINES TERMINATED BY '\r\n'
(column1, column2, @var1, column4, @var2) -- specify actual field names
SET column3 = REPLACE(@var1, ',', ''), column5 = REPLACE(@var2, ',', ''); -- remove thousand separators
