Can the applicant delete the claims at the time of national phase entry?

Yes, the applicant can delete the claims at the time of national phase entry.

Prior to The Patent Rules, 2003 as amended by (Amendment)Rules, 2016, it was required that the claim fee shall be paid in accordance with the number of claims in the PCT application. Further, the deletion of claims was permitted only by filing a separate request for amendment along with applicable official fee. Said provision has now been revoked. The applicant can now delete claims without paying said claim fee.