In this case you need not raise any invoice, inform transporter about the loss caused and deduct the amount to be paid from his bills. If your transporter is registered and opted for forward charge he will raise Credit note and issue to you.
And if the transporter is unregistered who falls under RCM ( most of the transporters falls under this), you have to raise a credit note against the RCM invoice (consignment note raised under sec.9(3) of the Act with full value) with applicable tax rate for the amount of deduction being made.
The rate of tax is 5% on GTA services.
Dear Experts, pls clarify if i miss something..