Dear Suman
Since the Sri Lankan Company does not have a PAN is India, Section 206AA of the Income Tax Act, 1961 is applicable (Introduced with effect from April 01, 2004) according to which TDS is to be deducted at the higher of the following rates: -
1. at the rate specified in the relevant provision of this Act; or
2. at the rate or rates in force; or
3. at the rate of twenty per cent.
In your case, TDS was supposed to be deducted at 20.6% (including surcharge) under Section 195 and Return is to be filed wherein it is mentioned that PAN is not available.
Once the return is filed with the NSDL after 15 days you can issue Form 16A from the NSDL website itself.
The Sri Lankan Company will utilise the credit available as per the tax laws of Sri Lanka. Indian Company need not bother.