The meeting is significant as the central government is planning to introduce a fresh version of the Bill in the winter session of Parliament, which starts on November 18.
In fact, Shah had announced the government would introduce the Bill before the National Register of Citizens.
In a statement via WhatsApp, the Chief Minister said views of all stakeholders must be taken into consideration with regard to the Bill.
"The Home Minister expressed his willingness to meet all stakeholders to discuss and garner views on the subject and also told the state government to initiate steps to coordinate with the Centre in this regard," it said.
The Bill seeks to fast-track Indian citizenship to Hindus, Sikhs, Buddhists, Parsis, Christ and Jains from Bangladesh, Pakistan and Afghanistan who entered India till December 31, 2014.
The Bill, passed by the Lok Sabha, lapsed in February, after it was not tabled in the Rajya Sabha following protest by several NDA allies and other social organisations in the north-eastern states.
At the meeting, Sangma also took up the amendment to the Sixth Schedule. "The Home Minister has asked the state government to put forth their issues in writing. Conrad also discussed various concerns raised by the committee for the amendment to the Sixth Schedule," the statement noted.
Sangma, also the national president of the National People's Party, discussed with Shah the political situation unfolding in Manipur and "hoped for an early solution".
The NPP, which has four members in the Manipur Assembly, is supporting the BJP-led government headed by Biren Singh.
( With inputs from IANS )