If the inward remittance received is less than the invoice amount raised for the export of services, the exporter needs to account for the shortfall appropriately in line with the applicable GST provisions. The invoice amount reflects the value of the export, and the export of services is generally considered a "zero-rated supply" under GST, which means no GST is levied on the export. However, there is a requirement to receive the full value of the export consideration within a specific time frame, typically within one year from the date of the invoice.
Regarding the third-party processor fee charged for remitting the payment, it does not affect the amount received under the Letter of Undertaking (LUT) for export without payment of tax. The export value is determined by the actual remittance received, i.e., the amount credited to the exporter’s bank account (which is $900 in your example). The $100 processor fee is considered a separate cost and should not be deducted from the value of the export when filing the LUT or calculating the GST-related obligations.
If there is a shortfall, such as the $100 in your example, the exporter needs to demonstrate that the full invoice amount is received within the one-year period. If the shortfall is due to a third-party processing fee, it will likely not trigger an issue under GST, as the actual amount received ($900) is still part of the export transaction. However, the exporter should ensure that the remittance receipt includes details of the fee to support the actual receipt amount.
Interest or penalties would not typically apply under GST if the shortfall is clearly due to the third-party processing fee, as long as the actual payment received is consistent with the invoiced amount. This should be substantiated with proper documentation like the FIRC (Foreign Inward Remittance Certificate) and bank statements/e-BRC.