The US National Security Agency may have accessed computers within the Indian embassy in Washington and mission at the United Nations in New York as part of a huge clandestine effort to mine electronic data held by its south Asian ally.

Documents released by the US whistleblower Edward Snowden also reveal the extent and aggressive nature of other NSA datamining exercises targeting India as recently as March of this year.

The latest revelations – published in the Hindu newspaper – came as Manmohan Singh, the Indian prime minister, flew to Europe on his way to the US, where he will meet President Barack Obama.

The NSA operation targeting India used two datamining tools, Boundless Informant and Prism, a system allowing the agency easy access to the personal information of non-US nationals from the databases of some of the world's biggest tech companies, including Apple, Google, Microsoft and Yahoo.

In June, the Guardian acquired and published top-secret documents about Boundless Informant describing how in March 2013 the NSA, alongside its effort to capture data within the US, also collected 97bn pieces of intelligence from computer networks worldwide.

The largest amount of intelligence was gathered from Iran, with more than 14bn reports in that period, followed by 13.5bn from Pakistan. Jordan, one of America's closest Arab allies, came third with 12.7bn, Egypt fourth with 7.6bn and India fifth with 6.3bn.

Though relations between India and the US were strained for many decades, they have improved considerably in recent years. President George Bush saw India as a potential counterweight to China and backed a controversial civil nuclear agreement with Delhi. Obama received a rapturous welcome when he visited in 2010, though concrete results of the warmer relationship have been less obvious.

According to one document obtained by the Hindu, the US agency used the Prism programme to gather information on India's domestic politics and the country's strategic and commercial interests, specifically categories designated as nuclear, space and politics.

A further NSA document obtained by the Hindu suggests the agency selected the office of India's mission at the UN in New York and the country's Washington embassy as "location targets" where records of Internet traffic, emails, telephone and office conversations – and even official documents stored digitally – could potentially be accessed after programs had been clandestinely inserted into computers.

In March 2013, the NSA collected 6.3bn pieces of information from internet networks in India and 6.2bn pieces of information from the country's telephone networks during the same period, the Hindu said.

After the Guardian reported in June that Pm program allowed the NSA "to obtain targeted communications without having to request them from the service providers and without having to obtain individual court orders", both US and Indian officials claimed no content was being taken from the country's networks and that the programs were intended to aid "counter-terrorism".

Syed Akbaruddin, an external affairs ministry spokesperson, said on Wednesday there was no further comment following the latest revelations.

Siddharth Varadajaran, editor of the Hindu, said the Indian government's "remarkably tepid and even apologetic response to the initial set of disclosures" made the story a "priority for Indians".

A home ministry official told the newspaper the government had been "rattled" to discover the extent of the the programme's interest in India. "It's not just violation of our sovereignty, it's a complete intrusion into our decision-making process," the official said.

Professor Gopalapuram Parthasarathy, a former senior diplomat, said no one should be surprised by the Hindu's story. "Everybody spies on everyone else. Some just have better gadgets. If we had their facilities, I'm sure we would do it too. The US-Indian relationship is good and stable and if they feel India merits so much attention then good for us," he told the Guardian.

Others have been less phlegmatic. Gurudas Dasgupta, a leader of the Indian Communist party, asked the government to raise the issue with Obama.

Anja Kovacs of the Delhi-based Internet Democracy Project said the articles showed that such datamining was not about any broader "struggle to protect society as a whole through something like fighting terrorism, but about control".

The Hindu argued that "the targeting of India's politics and space programme by the NSA busts the myth of close strategic partnership between India and US", pointing out that the other countries targeted in the same way as India "are generally seen as adversarial" by Washington.