Have you turned off index updating while importing (I don't know if navicat does this for you)? Turning index updating off will probably make your import take closer to linear time...
"ALTER TABLE tab DISABLE KEYS" turns off (non-unique) index updating for MyISAM tables. I don't know about InnoDB. If you are sure that you have no duplicates in the data you import it is probably faster to drop indices and re-create them after the import is done (if you import into empty tables at least).
And yeah, don't forget to "ALTER TABLE tab ENABLE KEYS" after the import, if you have disabled them prior.