The Gangs Matrix compiled by Scotland Yard is shared with local councils and other agencies.
But from a total of 3,806 people on the register, 1,500 are assessed as posing no risk of violence.
And a report by Amnesty international described it as “racially discriminatory” and said it breached international human rights law.
Amnesty found that the number of black men on the Matrix is disproportionate.
Figures from July 2016 showed that 87% of the people listed were black, Asian and minority ethnic, and 78% were black.
For London as a whole, 13% of the population is black, and police figures show 27% of those prosecuted for youth violence are black.
The charity’s UK Director Kate Allen said: “There is clearly a huge problem with knife crime violence at the moment in London, but the Gangs Matrix is not the answer.
“It’s part of an unhelpful and racialised focus on the concept of gangs. Put simply, it’s the wrong tool for the wrong problem.”
Black rights campaigner Stafford Smith told Sky News the register stigmatises youngsters who are on the database simply by association and not because they have done anything wrong or illegal.
“Our community needs a police service to stop the murders but the community won’t engage with the police if they are forever coming up with oppressive forms.
“The Matrix reaffirms to the community that there is an institutionalised way of policing. It doesn’t work, it just further marginalises this group of kids.”
The Amnesty report claims being on the Matrix could affect access to services such as housing, education and the job centre.
Researchers heard some families were threatened with eviction if a young person did not change their behaviour, and one was sent an ultimatum more than a year after their son had died.
The Metropolitan Police has defended the use of the database insisting its aim was to “reduce gang-related violence and prevent young lives being lost”.
In a statement it said: “Some young people identified as part of a gang may not yet have been drawn into gang violence.
“These individuals will be offered support to divert them away from activity that may result in either violent offending or them becoming a victim.
The Matrix was set up in 2012 in the wake of the wave of rioting that hit London and several other parts of the UK in the summer of 2011.
Police gather various intelligence including history of violent crime, entries on social media and information from bodies including local councils to identify gang members, then use a secret algorithm to calculate a risk of harm score set on a traffic light scale.
Figures from October 2017 showed the whole Matrix contained 3,806 entries, with 5% in the red category, the highest risk of committing violence, and 64% in the green, the lowest.
James Dipple-Johnstone from the Information Commissioner’s Office said: “We are in contact with the Metropolitan Police Service as part of an investigation into their use of a ‘gangs database’.
“As part of this, we’re considering how the database is used and if any aspects of it constitute a breach of the Data Protection Act.”
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Amnesty also called on the influential Commons Home Affairs Select Committee to investigate the use of police gang databases across the country.
It is understood that officers in Nottingham, Manchester and Birmingham gather similar information on gang links.