Almost once in 2 weeks,i am facing mysql data loss in a table. almost 600 rows are being deleted. I cant trace that issue.
What may cause this or how can i trace who/what makes it ?
Check out aspersa's 'stalk' and 'collect' tools: http://aspersa.googlecode.com/svn/html/stalk.html. Smart use of those should eliminate the need to enable the general query log, which probably gathers way too much data in two weeks to justify.
Other then that: tell us more about your setup: do you run replication? What kind of applications? Who has what kind of access? Do you have any suspects?
In addition to the above steps, I'd also recommend doing a comprehensive audit of your grants to see what user accounts might have access to this database that shouldn't have access.