Hi,
1. First of all stop all your connections on your database.
2. Modify the key_buffer_size at 1G or more ... if you have RAM

3. use Load Data from mysql console because is much faster (is uploading first time the data and after that is putting the indexes)
4. Try throwing an exclusive lock on the table before loading the data.
5. Add more memory on that server ... only for this operation !
I hope this is helpful

Regards