According to a report by French website Mediapart, this racial profiling took place between 2013 and spring of this year.
The report says PSG's former chief scout in France, Marc Westerloppe, told his colleagues that "there is a problem with the direction of this club… there are too many West Indians and Africans in Paris".
The claims are based on documents provided by the Football Leaks platform.
PSG scouts, the report claims, were asked to choose one of four options for every player they watched on an electronic form: French, North African, black African or West Indian.
According to Mediapart, this system prompted an internal investigation in 2014 when one scout, Serge Fournier, described Yann Gboho, a French teenager who was born in the Ivory Coast, as 'West Indian'.
It is claimed he did this because PSG "didn't want us to recruit players born in Africa, because you are never sure of their date of birth".
Fournier also told the website that the drop-down menu on the electronic form "should have said white instead of French", as all the players the national scouts recommended were French.
Gboho now plays for Rennes.
A spokesman for PSG, however, said the club started a new investigation into these claims three weeks ago.
But the French champs disputed the suggestion that recording players' racial backgrounds was still happening this year.
The spokesman said: "We are talking about one recruiting unit with a manager who put that in place from 2013 until 2017, without our knowledge.
He then added that "all these people have left" the club.
Westerloppe now has a youth development role at Rennes, where Gboho plays and where PSG's former sports director Olivier Letang is now president.
Supporters of PSG have reacted angrily to the Mediapart report on social media, pointing out that PSG's youth teams are predominately black.
But the case does have parallels with another Mediapart story in 2011.
This revealed an apparent plan by the French Football Federation to limit the number of black and North African players in its youth system.
That story almost cost former Manchester United defender Laurent Blanc his job as France manager, although he would quit a year later after a disappointing Euro 2012 campaign.
Claims of racism within their scouting system have come during a tough week for PSG.
The Qatari-owned club has also been accused of trying to cheat European football's Financial Fair Play rules by artificially inflating sponsorship deals – allegations it has strongly denied.
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