You need to give us more details. Where are you getting these timeouts? Whats your application doing? Does it involve EJBs? And what do you see in the log files?
You can increase the JTA trasaction timeout configuration in the application servers to a higher value. But as Jaikiran said, more details on this issue can provide you with a better help.
I would also like to know which application server you are using and what kind of scenario or use case this is happening.
