The disclosure came amidst protests, some of them violent, in different parts of the country against the Citizenship (Amendment) Act, which seeks to grant Indian citizenship to non-Muslim migrants from these three neighbouring countries.
As many as 2,830 people from Pakistan, 912 from Afghanistan and 172 from Bangladesh have been given Indian citizenship in the past six years and hundreds of them were Muslims, the official said, adding that such migrants will continue to get Indian citizenship if they fulfil eligibility conditions.
The Citizenship (Amendment) Act does not target any religious community from abroad, he asserted.
Those opposed to the law have objected to making religion as the basis of granting citizenship.
The official said Muslims are the majority community in these neighbouring countries and they will continue to get Indian citizenship if they fulfil eligibility conditions already provided in the law for registration or naturalisation.
Besides the 4,000-odd people, about 14,864 Bangladeshi nationals were also granted Indian citizenship after incorporating more than 50 enclaves of Bangladesh into Indian territory post the boundary agreement between the two countries in 2014, the official said.
According to the CAA, members of Hindu, Sikh, Buddhist, Jain, Parsi and Christian communities who have come from Pakistan, Bangladesh and Afghanistan till December 31, 2014 and facing religious persecution there will not be treated as illegal immigrants but given Indian citizenship.
The Act got the approval of the Parliament and assented by the President earlier this month.
The Citizenship (Amendment) Bill has been in public domain since 2016. It was cleared by a 30-member parliamentary committee consisting of Lok Sabha and Rajya Sabha members.
The present Act is broadly based on the same Bill.
By amending the appropriate rules during 2015-16, the government of India had already legalised entry as well as stay of such foreign migrants belonging to six minority communities from these three countries who had come into India up to December, 2014 because of persecution on grounds of religion.
The government of India had made such migrants also eligible for grant of Long Term Visa (LTV) to stay in India for a long time.
The CAA now enables them to take Indian citizenship if they fulfil conditions/qualifications for such citizenship provided they migrated from these three countries before December 31, 2014.
Another official said on different occasions special provisions have been made by the government of India in the past to accommodate the concerns of stay and citizenship of foreigners of Indian origin who had to flee to India.
For example, Article 6 of the Constitution of India provides that a person who has migrated to India from Pakistan before July 19, 1948 shall be deemed to be Indian citizen.
Secondly, even if he has migrated on or after this date he was registered as Indian citizen after staying for only six months in India.
Similarly, 4.61 lakh Tamils of Indian origin were given Indian citizenship during the years 1964-2008 after signing of international agreements in 1964 and 1974 between the two countries.
Presently, about 95,000 Sri Lankan refugees are living in Tamil Nadu. They are being given rations, doles and other facilities by the central and state governments.
They can apply for Indian citizenship as and when they become eligible to do so.
During 1962-78, more than two lakh Burmese of Indian origin fled from Burma after many trades and businesses were nationalised there and properties of such Indians were forcibly taken by the State.
They were settled in various parts of India.
In 2004, the central government delegated the power to grant citizenship by registration to six collectors of Gujarat and Rajasthan states and the government of Gujarat in respect of Hindu migrants displaced due to 1965 and 1971 wars or those Hindu migrants who had migrated from Pakistan five years before.
This delegation of power was initially for one year but the same was extended for another year in 2005 and then again in 2006.
The CAA does not target any religious community from abroad. It only provides a mechanism for some migrants who may otherwise have been called "illegal" depriving them of opportunity to apply for Indian citizenship provided they meet certain conditions, the official said.
The central government will frame rules to operationalise the provisions of the CAA.
No migrant from these communities will become Indian citizen automatically. He will have to apply online and the competent authority would see whether he fulfils all the qualifications for registration or naturalization as Indian citizen, the official said.