The Indian federal government is trying to deport Rohingya Muslims over their alleged “terror ties”, as the ethnic minority faces a brutal military crackdown in Burma that the UN has said could amount to ethnic cleansing.

The Indian supreme court is currently hearing an appeal lodged on the behalf of the estimated 40,000 Rohingya to save them from a plan by Prime Minister Narendra Modi’s Hindi nationalist government to expel them.

The country's home ministry has submitted an affidavit to the court saying it could confidentially share intelligence information with the Supreme Court showing Rohingya links to Isis and Pakistani militants.

An estimated 400,000 Rohingya have fled to Bangladesh to escape persecution in Burma since the start of a crackdown there on 25 August.

The offensive, which the United Nations branded a “textbook example of ethnic cleansing”, has seen desperate refugees climbing over barbed wire border fences to escape an alleged campaign of rape and murder by Burmese soldiers in the western state of Rakhine.

Reports have emerged that the Burmese military are laying landmines along the border to stop them coming back.

But in India, the government said it had reports from security agencies and other authentic sources "indicating linkages of some of the unauthorised Rohingya immigrants with Pakistan-based terror organisations and similar organisations operating in other countries."

It also said there was information on Rohingya involvement in plots by Isis and other "extremist groups" to ignite communal and sectarian violence in India.

Rohingya refugees – in pictures Show all 15 1 /15 Rohingya refugees – in pictures Rohingya refugees – in pictures A young girl and a baby wade through mud after arriving in Whaikhyang, Bangladesh from Burma on 10 September Dan Kitwood/Getty Images Rohingya refugees – in pictures Rohingya refugees walk through a camp in Whaikhyang, Bangladesh after arriving from Burma Dan Kitwood/Getty Images Rohingya refugees – in pictures A young Rohingya refugee gathers firewood after arriving in Whaikhyang, Bangladesh from Burma Dan Kitwood/Getty Images Rohingya refugees – in pictures Rohingya refugees wait for sacks of rice to be distributed in Whaikhyang, Bangladesh Dan Kitwood/Getty Images Rohingya refugees – in pictures Rohingya Muslim refugees arrive on a boat in Whaikhyang, Bangladesh after crossing from Burma on 8 September Dan Kitwood/Getty Images Rohingya refugees – in pictures Rohingya Muslim refugees react after being re-united with each other after arriving in Whaikhyang, Bangladesh on a boat from Burma Getty Rohingya refugees – in pictures Rohingya Muslim refugees walk along the remains of a road after arriving in Whaikhyang, Bangladesh on a boat from Burma Dan Kitwood/Getty Images Rohingya refugees – in pictures Rohingya Muslim refugees wade through water after arriving in Whaikhyang, Bangladesh by boat from Burma Dan Kitwood/Getty Images Rohingya refugees – in pictures Rohingya Muslim refugees wade through water after arriving in Whaikhyang, Bangladesh by boat from Myanmar Dan Kitwood/Getty Images Rohingya refugees – in pictures Rohingya Muslim refugees stand in the rain after arriving in Whaikhyang, Bangladesh by boat from Burma Dan Kitwood/Getty Images Rohingya refugees – in pictures Indian children hold placards and shout slogans during a protest against the alleged persecution of the Rohingya Muslims in Burma EPA/Raminder Pal Singh Rohingya refugees – in pictures Supporters of the Difa-e-Pakistan Council (DPC), an Islamic organisation, listen to their leaders' speeches against Burma's persecution of Rohingya Muslims, during a demonstration in Karachi Reuters/Akhtar Soomro Rohingya refugees – in pictures Hundreds of Iranians take part in a protest against violence in Myanmar after weekly Friday prayers, in Tehran EPA/Abedin Taherkenareh Rohingya refugees – in pictures Indonesian Muslim activists hold placards and shout slogans during a protest against the alleged persecution of the Rohingya minority in Magelang, Central Java, Indonesia EPA/Ali Lutfi Rohingya refugees – in pictures Members of an Islamic organisation shout slogans against the Burma government during a protest in Dhaka, Bangladesh EPA

Senior home ministry official Mukesh Mittal said the Indian government would privately show the court material gathered from "sensitive investigations" to substantiate the claims in its affidavit.

They said the 40,000 Rohingya had arrived in India illegally four or five years ago from Bangladesh after fleeing Burma.

In a separate development, Indian police say they have arrested British national Shauman Haq, 27, near a bus stop in Delhi on Sunday and allege that he had come to India via Bangladesh specifically to recruit Rohingya to fight for al-Qaeda.

Rohingya in India voiced worries that they were being unfairly tainted by the allegations and sought more understanding for their plight.

"We feel helpless and hopeless," said Rohingya youth leader Ali Johar, who came to India in 2012 and lives with his family in a Delhi settlement.

"The world's largest democracy has given us shelter but they should handle this situation more empathetically."

Mr Modi's government has been criticised by activists for not speaking out against Burma's offensive against the Rohingya and right-wing groups in India have begun vilifying Rohingya living there.

The Rohingya are denied citizenship in Buddhist-majority Burma and regarded as illegal immigrants, despite claiming roots that date back centuries. More than 800,000 Rohingya currently live in Bangladesh.