The youths were detained as they shouted slogans and waved black flags and banners demanding Special Category Status to Andhra Pradesh during the rally near JNTU Kakinada campus, police said.
Naidu had to wind up his speech because of a sudden downpour.
AP Deputy Chief Minister N Chinarajappa, MPs Thota Narasimham, Pandula Raveendrababu, Muralimohan, state Health Minister Kamineni Srinivas, MLAs Kondababu and P Ananta Laxmi were present at the meeting.