Hi Ramana,
If you could tell us on which table you're actually querying and also the where conditions you've specified. It also depends on the number of table entries but we can't say that NE operator will cause performance issue.
Are you using all the primary keys in WHERE condition? If so you can retrieve the records first and later can use DELETE statment on internal table for entries which you don't want instead of using NE operator in select statement
Best Regards,
Lakshman