For TDS aspect on payment made to transporters, the limits are Rs.30,000 for single transport voucher or Rs.75,000 of transport expense per transporter per annum.
if total PAYMENT/CREDIT to transporter exceeds these limits then TDS provisions apply.
Section 206A for TDS at higher rate for not submission of PAN applies to the transactions on which tax is deductible under Chapter XVIIB.In case of transport contract TDS is required to be deducted if single payment exceed 30000/- or sum of total payment to single person exceed 75000/- in a year.In your case if single pmt doesnot exceed 30000/- or if aggregate of all payments is not going to exceed 75000/- then you are not liable to deduct tax @ 20%