"We tried to convince the Centre that the bill was against the Assam Accord and will nullify the ongoing updating of the National Register of Citizens", Bora told reporters after the meeting.
A year ago the Assam government published a draft citizens' register that left off 4mn people unable to prove they were living there before 1971.
Protesters in Assam set up blockades with burning tires and vandalized two BJP offices, disrupting traffic and business from early in the morning to late afternoon.
Assam Finance Minister Himanta Biswa Sarma on Tuesday said that the issue of granting citizenship to Hindu refugees from Bangladesh and Pakistan can be resolved only through religion, not secularism.
"Six tribal youths while demonstrating against the Citizenship (Amendment) Bill turned violent at Madhab Bari in western Tripura".
AGP chose to snap ties with the BJP over the Citizenship Bill, which they say will make the Assam Accord "meaningless".
Members of Asom Yuba Chatra Parishad staged a nude protest against the Bill at Tinsukia in Upper Assam, and in Delhi, too, some of the demonstrators stripped naked outside Parliament.
He also said that Muslims have been left out of the minorities covered under the bill's provisions.
Soon after Prime Minister Narendra Modi announced that his government is planning to push the Citizenship Bill, protests broke out across Assam on Saturday, with effigies of PM Modi being burnt at several places.
Three AGP ministers in the state cabinet - Bora (agriculture), Keshab Mahanta (water resources) and Phanibhushan Choudhury (food and civil supplies) - will tender their resignations and complete the other related formalities on Wednesday, the party chief said. Congress said many states opposed the bill and demanded that it should be sent to a select committee, walking out after the government did not heed its demand.
The opposition Congress and the All Indian United Democratic Front (AIUDF) have 25 and 13 members respectively.
Withdrawal of the AGP, which has 14 MLAs in the 126-member assembly, would not have any immediate effect on the future of the Sarbananda Sonowal-led government that still has the backing of 74 MLAs. "The proposed amendment will make these persecuted migrants eligible to apply for citizenship", Rajnath Singh said.
The Lok Sabha on Tuesday passed a contentious bill seeking to provide Indian citizenship to non-Muslims from Bangaldesh, Pakistan and Afghanistan, amid protests in north eastern states and opposition parties terming the proposed law "divisive" and "flawed".
The NDA government introduced the bill in the Lok Sabha on 19 July 2016 - the aim was to amend the Citizenship Act, 1955.
JD (U) national general secretary Sanjay Verma said his party will oppose the bill because it will do no good to the identity and culture of Assam and the northeast.
The Congress, TMC, CPI-M and a few other parties are opposing the bill claiming that citizenship can't be given on the basis of religion.
The BJP leader maintained that his party isn't the first to take up the cause of Hindu refugees.
The bill seeks to give citizenship to Hindus, Sikhs, Jains, Buddhists, Christians and Parsis from Afghanistan, Pakistan and Bangladesh, who came to India before December 31, 2014.
Another BJP ally Shiv Sena voiced support for AGP's decision to snap ties with the saffron party on Monday.