The tricolour flying atop the Indian High Commission in London was grabbed at by a group of protesters waving separatist Khalistani flags and chanting pro-Khalistani slogans on Sunday, leading to an arrest related to the violent disorder.
Officials from the mission said the "attempted but failed" attack had been foiled and that the tricolour was now flying "grander".
Scotland Yard said it was called to reports of disorder on Sunday afternoon and that a man has been arrested as its enquiries continue.
"There was no report of any injury, however windows were broken at the High Commission building," the metropolitan police statement said.
"Officers attended the location. The majority of those present had dispersed prior to the arrival of police. An investigation was launched, and one male was arrested nearby a short time later on suspicion of violent disorder. Enquiries continue," the statement said.
India has meanwhile registered its strong protest with the British government over the safety of its diplomatic mission and questioned the lack of sufficient security at the premises.
Images of shattered windows and men climbing the India House building were circulating on social media and videos from the scene show an Indian official grabbing the flag from a protester through the first-floor window of the mission, while the protester is seen hanging off its ledge and waving a Khalistan flag before it is taken away.
The MEA said the senior-most UK diplomat in New Delhi was summoned late evening on Sunday to convey India's 'strong protest' at the actions taken by separatist and extremist elements against the Indian high commission in London.
"An explanation was demanded for the complete absence of the British security that allowed these elements to enter the High Commission premises. She was reminded in this regard of the basic obligations of the UK government under the Vienna Convention," the MEA statement said.
"India finds unacceptable the indifference of the UK government to the security of Indian diplomatic premises and personnel in the UK. It is expected that the UK government would take immediate steps to identify, arrest and prosecute each one of those involved in today's incident, and put in place stringent measures to prevent the recurrence of such incidents," it said.
The banned terrorist organisation, Sikhs For Justice, is conducting a so-called "Referendum 2020" amid a crackdown on pro-Khalistan leader Amritpal Singh in Punjab.