Visiting the Jallianwala Bagh memorial on Wednesday, Khan paid his respects to those who lost their lives in the massacre and extended his "own apologies", according to a statement on the London mayor's website.
During a visit to the Jallianwala Bagh memorial and garden, the Mayor paid his respects to those who were killed there in 1919, and made it clear that, nearly 100 years on from the terrible event, the British Government should formally apologise on behalf of the British politicians of the time.
On April 13, 1919, Colonel Reginald Dyer had ordered firing on peaceful protesters and Baisakhi pilgrims assembled at Jallianwala Bagh.
The Mayor of London, Sadiq Khan, said, "The Jallianwala Bagh massacre is one of the most horrific events in Indian history". "Our thoughts are with all those who died", he wrote.
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The Punjab chief minister said he heard Khan's remarks on the Jallianwala incident and was happy to know about his feelings on the matter.
In October, Mayor Sadiq Khan, whose grandparents were born in India and parents migrated from Pakistan to United Kingdom, said he would visit India and Pakistan to promote the British capital as a destination of choice for trade and cultural ties.
Former British PM David Cameroon visited Jallianwala Bagh in February 2013 and offered regrets over the killings, stopping short of a formal apology.
Colonial-era records show about 400 people died when soldiers opened fire on men, women and children in the enclosed area, but Indian figures put the toll at closer to 1,000.
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"As the former British Minister said when he visited the Jallianwala Bagh in 2013, the massacre was a deeply shameful act in British history and one that we should never forget".
Mr Khan also visited the Langar hall, the largest community kitchen in the world, of the shrine complex and partook langar while sitting on the floor.
The Shiromani Gurdwara Parbandhak Committee (SGPC) gave Mr Khan a "siropa" (robe of honour) during the visit.
Khan, who was on a three-city tour of India, visiting Mumbai, New Delhi and Amritsar, later crossed over to Pakistan from the Attari-Wagah land border. On Thursday he is in Islamabad and is scheduled to visit Karachi before he returns to London.
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