Dear Deepak Ji,
As per Section 194C of the Income Tax Act, any person who are responsible for paying the sum to the contractor (transporter in your case) would be liable to deduct the TDS at the rate in force.
Now coming to your case specifically, you are only reponsible FOR PAYING the sum to the transporter. it wud doesn't make any difference in the eyes of IT Law that you recover the said sum from the vendor lateron.
Therefore I am of the strong opinion that in your case you organisation is being liable to collect the pan no of transporter and disclose the same in your E TDS Return.
Pl contact me for any further clarification in this regard.
CA Karan Malhotra
M No 9999098408
kkmalhotra08 @ gmail.com