The Home Minister said the migrants - Hindus, Jains, Christians, Sikhs, Buddhists and Parsis - were earlier given protection against legal action in 2015 and 2016 and citizenship will be given only after due scrutiny and recommendation of district authorities and the state government. "Even BJP leaders in Assam have always spoken on the issues related to the indigenous people", he added.
The Bill endorses citizenship for all religious minorities from neighbouring Bangladesh, Pakistan and Afghanistan.
A new registry of citizens compiled in Assam this year forced the state's 33 million people to submit documents proving they were there before 1971, when millions fled Bangladesh's independence war. Later, opposing the bill, members of Congress and TMC staged a walkout.
The AGP had entered into an alliance with the BJP before the 2014 polls and was opposed to the Bill since the beginning.
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.
"We have been agitating against the Bill for quite some now and with the Centre apparently intent on getting the proposed legislation passed, we have decided that we will return the awards that were conferred on the martyrs in 2016 by the state government here", Rajen Deka, president of the Parishad, formed in 1989, told The Shillong Times on Tuesday.
In the 126-member Assam Assembly, the AGP has just 14 MLAs, while the ruling coalition, which now comprises the BJP with 60 MLAs and Bodoland People's Front (BPF) with 12 MLAs, has a comfortable majority.
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.
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Most Northeast parties, including the allies of BJP, opposition Congress and Left parties have strongly opposed the bill, saying "it is against the spirit of the Constitution".
The IPFT is also a member of Bharatiya Janata Party-led alliance NEDA (North East Democratic Alliance), convener of which is BJP-led Assam government's powerful minister Himanta Biswa Sarma. He also clarified that the government had acceded to the opposition demand for implementation of Clause 6 of the Assam Accord, to grant tribal status to six OBC communities - Tea Tribes /Adivasi, Tai-Ahom, Chutia, Koch-Rajbongshi, Moran and Motok. "Withdraw this bill. If you can't do it, reconstitute the committee", he said.
In a statement here earlier in the day, AGP leader and former chief minister Prafulla Kumar Mahanta said the party would withdraw support to the government in the state if the Citizenship Amendment Bill, 2016 is passed by Lok Sabha.
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The Congress, TMC, CPI (M) and a few other parties have been steadfastly opposing the bill claiming citizenship can not be given on basis of religion, as India is secular.
"We tried our best to convince the Modi government not to pursue the Bill that goes against the constitutional provisions, besides being potentially risky for the indigenous people of Assam".
Another BJP ally Shiv Sena voiced support for AGP's decision to snap ties with the saffron party on Monday.