MYSQL query performs very slow

I have developed a user bulk upload module. There are 2 situations, when I do a bulk upload of 20 000 records when database has zero records. Its taking about 5 hours. But when the database already has about 30 000 records the upload is very very slow. It takes about 11 hours to upload 20 000 records. I am just reading a CSV file via fgetcsv method.