Hi Umesh,
As we know it's a known issue, public KB is available for the same.
http://www.symantec.com/docs/TECH144817
Symantec next release i.e. SEP 12.1 RU2 should have fixed to this problem.
Meanwhile could you check with following workaround:
Can you set the value of securitynotifytask.notifcation.interval to 59 in conf properties?
Add the following line to conf.properties.
scm.securityalertnotifytask.notification.interval=59
This change should create delay in multiple email response.
Also you can test it with SEP 12.1 RU2 beta version.
https://symbeta.symantec.com/login.html
If beta version did not resolve the issue, please immediately log a case with Support.
I hope it helps.