Yes, you can join M.Tech Computer Science and Technology Course from Andhra University after a B.Tech in CSE from JNTUK. Curriculums of CSE and CST are both analogous to each other and provide the required  effective engineering education.

However it is always desired you join a Institute of Higher Repute for your Masters, as you have done B.Tech from JNTU Kakinada, and Andhra University is some what at par with it. You must prepare yourself for pursuing Masters from one of the Higher Technical Universities like Top IITs, NITs, BITS Pilani, IIITs or IIIT Delhi. The above institutes have excellent infrastructure, faculty and research facilities as far as CSE is concerned besides enjoying an excellent employer outlook.