Protesters burned tires and blocked highways and rail tracks in India's remote northeast for a second day on Wednesday as the upper house of parliament began debating legislation that would grant citizenship to persecuted Hindus and other religious minorities from Pakistan, Bangladesh and Afghanistan.

The bill was approved on Monday in the lower house, where Indian Prime Minister Narendra Modi's Hindu nationalist government enjoys majority support. The bill still needs the backing of smaller regional political groups in the upper house for it to become law.

The Press Trust of India reported that police fired rubber bullets and used batons and tear gas to disperse protesters in Dibrugarh district in Assam state on Wednesday. Street protests were also reported in Gauhati, the state capital.

The protesters organised an 11-hour shutdown on Tuesday saying they oppose the bill out of concern that more migrants who came to the country illegally will move to the border region and dilute the culture and political sway of indigenous tribal people.

Introducing the bill in the upper house, Home Minister Amit Shah said the bill was not anti-Muslim as it did not affect the existing path to citizenship available to all communities.

"It seeks to address the difficulties of Hindus and other minorities who suffered persecution in Muslim-majority Pakistan, Bangladesh and Afghanistan," he said.

Anand Sharma, a leader of the main opposition Congress party, said the bill was "discriminatory because India's constitution provides equal opportunities to all communities". Some opposition members complained the the bill excluded Tamil Hindus who fled Sri Lanka during the civil war.

Meanwhile, the US Commission on International Religious Freedom criticised the bill as going in a wrong direction, against India's rich history of secular pluralism and the Indian constitution, and sought American sanctions against Home Minister Shah if the bill is passed by both houses of Parliament.

India's External Affairs Ministry spokesman Raveesh Kumar said the US commission's statement “is neither accurate nor warranted.”

"The bill provides expedited consideration for Indian citizenship to persecuted religious minorities already in India from certain contiguous countries. It seeks to address their current difficulties and meet their basic human rights," Kumar said in as statement.

“Such an initiative should be welcomed, not criticised by those who are genuinely committed to religious freedom. “

After the bill was approved in India's lower house on Monday, Prime Minister Imran Khan criticised the legislation, saying it was "driven by a toxic mix of an extremist Hindutva ideology".

Meanwhile, in a statement issued by the Foreign Office Pakistan condemned the move and said it was in "complete violation of the Universal Declaration of Human Rights and other international covenants on elimination of all forms of discrimination based on religion or belief".