The case was earlier registered with the Special Cell of the Delhi Police.
Earlier, the Union Ministry of Home Affairs gave the nod to transfer the case to NIA.
The Special Cell of Delhi Police had registered an FIR in connection with the protest staged by pro-Khalistani activists at the Indian High Commission in London on March 19 during which the Tricolour was pulled down from the premises.
The case was registered after the Union Ministry of Home Affairs asked Delhi Police to take legal action.
The FIR was registered under relevant sections of Indian Penal Code, Unlawful Activities (Prevention) Act and Prevention of Damage to Public Property Act and an investigation has been initiated in the case.
The British Deputy High Commissioner was also summoned by the Centre, demanding an explanation over the complete absence of security during the protest.
The British High Commissioner to India, Alex Ellis had described the incident as “disgraceful” and “totally unacceptable”.