Aashima
As you told that you have taken an exemption certificate from IT Deptt that u have deduct TDS @ 3% , this notification has come effect when rate is 10% /20% . But now rate itself is 2% so you must deduct TDS @ 2% becasue exemtion certifcate is applicable by considering an assumption that other provision will remains same.
In this context you can communicate to IT deppt. to amend your exemption certificate.
Furthur i will tell you another example based on ur query............Let say "A" is tranporter & providing transport service to many companies. But "A" take an certificate from IT depptt for LOWER RATE OF TDS deduction . But now provison has been changed w.e.f 01/10/2009 that if transporter provides the PAN no. then no TDS .
In that case "A" must opt for providing PAN because provosion of income tax act automaticaaly gives relaxation to assesse........
Hope you have no doubts..........