Naidu, who has been campaigning against the Centre's apathy of giving special category status to Andhra Pradesh, met Akhil Gogoi on sidelines of a programme at Delhi's Vijay Chowk.
Assam has been witnessing a number of protests over the contentious Citizenship Amendment bill.
Prior to PM Modi's public rally held at Changsari in Assam on Saturday, six persons marched half-naked in front of the state secretariat, shouting slogans against the Citizenship bill.
Modi was also shown black flags in at least two places.
The Citizenship (Amendment) Bill seeks to provide Indian citizenship to Hindus, Jains, Christians, Sikhs, Buddhists and Parsis from Bangladesh, Pakistan and Afghanistan after six years of residence in India even if they do not possess any document.
The bill was passed by the Lok Sabha during the winter session on January 8 and has been awaiting Rajya Sabha nod.
READ: Interim budget passed by Lok Sabha