Transaction handling through java

I am facing the following problem.

Our  application sends a block of queries to postgres in a begin end block. If one of the queries take a long time to
finishthe whole transaction is assumed to be committed by the application even though the query is still running . This
resultsin failure of all subsequent transactions. 

Although the application is programmed to catch all exceptions , it somehow is not able to figure out that the
transactionis still not complete. 

I am using postgres 8.3

with regards

Nalini