As an intramural post doc in NLM, if I get K99 award, do I have to transfer to a different institution for R00 phase?

Yes, you'll have to secure an independent research position, preferably a tenure-track assistant professor position (or equivalent) at an eligible extramural institution, to activate the R00 phase. You may choose to apply for independent phase position within the NIH intramural research program (IRP). However, should you accept such a position in the IRP, the independent phase of the award will not be activated. This is because NIH intramural scientists are supported directly by NIH intramural funds and are not eligible for NIH extramural grant awards.