Scott was summoned to the foreign ministry on Sunday night.
"India finds unacceptable the indifference of the UK Government to the security of Indian diplomatic premises and personnel in the UK," the foreign ministry said in a statement, saying that a strong protest was lodged with Scott over the "actions taken by separatist and extremist elements" against the Indian mission in London.
The foreign ministry demanded an explanation as to why the British security "allowed these elements to enter" the mission premises and urged the British government to take steps to arrest those involved in the incident.
Earlier on Sunday, videos emerged on social media showing a group of supporters of the Khalistan separatist movement protesting outside the Indian mission in London. One of the protesters pulled down the Indian flag from the first-floor balcony of the building. The flag was replaced with a Khalistan flag.
The protesters were demanding the creation of a Sikh homeland named Khalistan, they allege that the government of Indian Prime Minister Narendra Modi crackdown on pro-Khalistan Sikh activists in Punjab is an act of repression.
It was later reported by The Guardian that one man was arrested in relation to the incident.
"Officers attended the location. The majority of those present had dispersed prior to the arrival of police," a Metropolitan Police spokesperson said as quoted by The Guardian on Sunday, adding that an "investigation was launched, and one male was arrested nearby a short time later on suspicion of violent disorder."
"Officers attended the location. The majority of those present had dispersed prior to the arrival of police," a Metropolitan Police spokesperson said as quoted by The Guardian on Sunday, adding that an "investigation was launched, and one male was arrested nearby a short time later on suspicion of violent disorder."
London Mayor Sadiq Khan said on Twitter that he condemned the violence and vandalism at the Indian high commission.