This is a very old and well-known problem.
There is no way to be absolutely certain a file being written by the FTP daemon is complete. It's even possible that the file transfer failed and then gets restarted and completed. You must poll the file's size and set a time limit, say 5 minutes. If the size does not change during that time you assume the file is complete.
If possible, the program that processes the file should be able to deal with partial files.