After setting up ganglia to collect stats and using jconsole, we narrowed down the problem to blocking threads.
The resolution was to increase the
mapred.job.tracker.handler.count from current value of 64 to 128
Our best assumption for the issue was that,All the Distcp mapper tend to complete at the same time, thereby blocking a lot of threads in cleanup process and freezing Job tracker for a good 10-15 minutes