Hi Srinivas,
How have you designed the scenario? Does it involve BPM? Are you using DOM parser in java mapping? BPM generally affects system performance. With the same payload which is causing the delay, please run the mapping in test tab. Is it taking same time or less? Complicated mapping logic might delay the processing. If you find in test tab the mapping is not taking that much time then you need to discuss the issue with BASIS team. There might be memory constraint in the server which needs to be eradicated.
Regards
Anupam