I do not believe you can buy certificates pre-embedded with RFID transponders. You could contact Hitachi about embedding its µ-chip (pronounced “mu-chip”) into new certificates that you create. The chip is very tiny and can be read from close-range (see Hitachi Unveils Smallest RFID Chip, Hitachi Unveils Integrated RFID Tag and RFID News Roundup: Hitachi Shrinks Smallest RFID Chip).
You might also consider affixing a label to standard certificates. The American University of Sharjah and dozens of other universities throughout the United Arab Emirates (UAE) are placing RFID tags on the diplomas they issue, in order to ensure the validity of the documents, as well as speed up the process of university registration (see UAE Universities Adopt RFID to Thwart Diploma Forgery). The labels have security features to ensure that they cannot be duplicated on bogus diplomas.
—Mark Roberti, Founder and Editor, RFID Journal