The Prime Minister posed for pictures in a bulldozer in Gujarat on Thursday after being taken on a tour by Lord Bamford, who has donated millions to the Conservatives.
But Mr Johnson faced a backlash on the taxpayer-funded two-day trip to India, as the nation’s supreme court ordered the demolitions in New Delhi to stop.
They were being carried out by an authority controlled by prime minister Narendra Modi’s Hindu nationalist Bharatiya Janata Party amid rising communal violence.
Footage of bulldozers pulling down buildings ran prominently on Indian TV news, as did video of Mr Johnson boarding a JCB bulldozer in the new factory in Gujarat.
He indicated he would bring up those issues during Friday’s talks with Mr Modi, who is accused of damaging of whipping up anti-Muslim sentiment.
The Prime Minister told broadcasters: “We always raise the difficult issues, of course we do, but the fact is that India is a country of 1.35 billion people and it is democratic, it’s the world’s largest democracy.”
Amnesty India said: “In the backdrop of Municipal Corporation of Delhi using JCB bulldozers to raze down shops of Muslims in Northwest Delhi’s Jahangirpuri yesterday, UK Prime Minister’s inauguration of a JCB factory in Gujarat is not only ignorant but his silence on the incident is deafening.
“As Indian authorities clamp down on human rights daily, the UK government must not remain a mute bystander.”
Mohamed Zeeshan, an Indian Muslim columnist, said Mr Johnson’s visit was “turning increasingly tone-deaf”.
“Only way Johnson can salvage this trip is by speaking up,” he said.
Downing Street denied it was a conflict of interest for the Prime Minister to meet a major Tory donor on the visit and stressed he was also seeing “a number of businesses, universities and science and tech firms”.
Asked if Mr Johnson was embarrassed to make the JCB visit as bulldozers destroyed Muslim properties, the Prime Minister’s official spokesman said: “I think this is predominantly a matter for the Indian authorities.”
Asked if Mr Johnson chose to visit the plant because Lord Bamford is a major donor, the official spokesman said: “No, he chose to go to the JCB factory because it’s a very good illustration of UK business.”