Khandu, who attended a consultative meeting on the proposed Bill, chaired by Shah, raised the concerns of the indigenous tribal communities and said Arunachal unequivocally opposed the CAB.
The Bill seeks to remove hurdles in the way of migrants from Bangladesh, Pakistan and Afghanistan from getting the Indian citizenship.
The BJP-led NDA government had introduced the Bill in its previous tenure but could not push it through due to protests by opposition and it lapsed following the dissolution of the last Lok Sabha.
The Bill is expected to be passed in the ongoing winter session.
During the meeting, the Chief Minister sought special provision to protect the interests of indigenous tribal communities of Arunachal, which should be in accordance with the public sentiments.
Union Sports and Youth Affairs Minister Kiren Rijiju, Deputy Chief Minister Chowna Mein, and leaders of different political parties and civil society groups also attended the meeting.
Khandu said the Home Minister assured that entire inner line permit regime of Arunachal Pradesh, including applicable provisions of the Bengal East Frontier Regulation 1873 and the Chin Hills Regulations 1896, would be suitably incorporated in the CAB.
Shah also assured the Arunachal delegation that there would be "zero impact to Arunachal Pradesh, to ensure the interest of indigenous people of the state."
"The Home Minister assured that the central government will consider all the concerns raised by them in the CAB to protect the interests of Arunachalees," Khandu said.
( With inputs from IANS )