NEW DELHI, India — Their offices raided, bank accounts frozen and travel restricted, international aid and rights groups with deep roots in India say they are struggling to operate under Prime Minister Narendra Modi, whose Hindu nationalist Bharatiya Janata Party has elevated the role of sympathetic homegrown social organizations while cracking down on foreign charities.

Greenpeace India, which has repeatedly pushed the government to address hazardous air quality in cities across India, said this month that it was forced to close two regional offices and sharply reduce its staff after its Benagaluru offices were raided and its bank accounts frozen.

Tax officials allege it was illegally receiving funds through a shell company set up to evade authorities after India’s home minister canceled the group’s license.

Amnesty International India, which has accused the Modi government of eroding freedom to dissent by jailing prominent critics, had to slash 68 jobs — 30 percent of its in-country workforce — and cancel programs after Finance Ministry officials carried out a 12-hour raid on its headquarters in November.

While the raid was underway, the government released a statement accusing the group of illegally receiving $3.5 million from an overseas account through a shell company.

Both Greenpeace and Amnesty International have denied the allegations.

International aid organizations have operated in India for decades, collaborating with the government on issues ranging from clean water to children’s education to disposal of e-waste.

The government no longer sees these groups as partners, activists and observers say, but rather as threats.

Critics say the government is attempting to cover up human rights failures by cracking down on groups that expose them.

“Government authorities are increasingly treating human rights organizations like criminal enterprises,” said Amnesty International India executive director Aakar Patel.

Vijay Khurana, secretary-general of the Confederation of Non-Governmental Organizations of India, supports the government crackdown on international organizations doing aid work with foreign funding.

“It has become a business for them. They misuse funds, land and other facilities provided by donors,” Khurana said, adding that the government should further encourage Indian organizations funded by local donors.

The Modi government has used the Foreign Contribution Regulation Act, which regulates foreign funding for civil society groups, to cut off funds and stymie activities of organizations that question its policies, rights activists say.

Since coming to power in 2014, the Modi government has canceled the licenses of nearly 15,000 charities, preventing them from receiving foreign funds, for failing to produce timely tax returns and other required documents, Junior Home Minister Kiren Rijiju told Parliament last year.

“There is complete intolerance to any kind of government criticism,” said Jayati Ghosh, an Indian economist who studies India’s human rights landscape.

At the same time, Hindu nationalist organizations, especially the Rashtriya Swayamsevak Sangh, or National Volunteer Corps, a hard-line Hindu group that Modi belongs to, have flourished, she said.

“Nothing happens to them if they get foreign funds. There is absolutely no kind of control on their activities,” Ghosh said.

John Dayal, a civil liberties activist and former president of the 16 million-member All India Catholic Union, said Christian charities with a longtime presence in India running programs in education, health and development in remote villages haven’t been spared in the crackdown.

Christian aid groups “cannot receive even small donations. Many have had to close down. Many hostels and medical centers have closed down. The people are the ones who suffer,” Dayal said.

Meenakshi Ganguly, South Asia director of Human Rights Watch, places the blame at the feet of the previous Congress party government for amending the Foreign Contribution Regulation Act in 2008 to require organizations to reapply for registration every five years — over the concerns of civil groups who said their operations would become subject to the whims of the government.

Ganguly said she has seen the Modi government’s aversion to scrutiny by foreign aid groups and agencies since it came to power in 2014. “The message is clear that the government wants to cover up human rights failures by cracking down on critics,” she said.

Last year, India refused to allow investigators from the Geneva-based office of the U.N. High Commissioner for Human rights to visit the Indian-controlled portion of Kashmir and investigate reports of rights violations in the disputed region.

India’s crackdown on international rights groups mirrors developments elsewhere in South Asia. In neighboring Pakistan, the government of Prime Minister Imran Khan has ordered more than a dozen international aid organizations to wind up their activities after determining they were “working against the interest of the state,” according to Pakistan’s Interior Ministry.

The groups include U.S.-based Catholic Relief Services, ActionAid U.K. and the Danish Refugee Council.

In India, Greenpeace and Amnesty International have responded to the setback with defiance.

“There are many things right in the country. I don’t think it is possible for one government or one man to shut down an organization like ours,” Patel said.