Finally found the solution after long debugging steps!
The problem is with the LaunchDaemon plist file ownership. If I copy plist from SSH the the file properties are as below
-rw-r--r-- 1 root wheel 461 Mar 3 15:20 com.Mycompany.Myapp.plist
If the LaunchDaemons copied by cydia the file properties are as below
-rw-r--r-- 1 503 staff 461 Mar 3 15:20 com.sourcebits.TsavoriteClient.plist
We need to change the LaunchDaemons plist file ownership before preparing the .deb file using the command
sudo chown -R root:wheel filePath