06 July 2012
first you paid amount to party not to transporter. so you don't need to deduct TDS. Moreover you have Transporter PAN also for safe side. As this freight for material inward then after getting PAN you don't need to deduct TDS. sec 194 C
07 July 2012
since you are not paying the Transportation charges directly to the transporter you are not liable to deduct TDS as you paying the amount to the party from whom you are purchasing therefore the party is liable to deduct TDS and if the Transporter gives PAN to party then no TDS is required but if you are paying the Transport and the case is not of Re-imbursement then you are liable and you have to obtain PAN
In your case deduction of TDS is not applicable as it is a case purchase which has only be accounted wrongly through Transportation Charges.
However, In case transportation charges are paid to a goods transport agency, TDS is required to be deducted at a higher rate of 20%, only in case transporter doesn't furnishes his PAN No. to the deductee. Otherwise, TDS is not required to be deducted on the same.