Yes, in certain circumstances specified under section 29(2) of the CGST Act, the proper officer can cancel the registration on his own. Such circumstances include: a person who contravene provisions of the Act; not filing return for a continuous period of six months (for a normal taxable person) or three returns (for Composition taxable person); registration has been obtained by means of fraud, and not commencing business within six months from the date of registration (in case of voluntary registration). However, before cancelling the registration, the proper officer shall give reasonable opportunity of being heard. (Section 29 (2)).
(ICAI FAQ PUBLICATIONS 06-09-2017 REGISTRATION: FAQ NO. 27)