Service Tax Dispute Related

One of our client's is in receipt of a Show Cause Notice for non payment of service tax. The background of the case is that the client is a sub-agent in the international and domestic air travel ticket booking industry. The client has neither charged nor collected service tax on it's commission/handling charges. The department seeks to tax the whole bill amount, i.e., ticket fares and handling charges as taxable turnover and recover service tax on the same. Our query is that whether there is any remedy to seek help from the department itself and make any application to the authorities and have the taxes levied only on the commission/handling charges portion of the bills and not on the ticket fares.