Plain clothes police officers targeted three inbound flights from countries where the practice is common.
The Met claimed the operation was educational and not stereotyping.
More than 2,000 suspected FGM victims received medical attention between April and June, but there has never been a conviction in the UK.
Det Ch Supt Ivan Balhatchet said: "This isn't about labelling, this isn't about stereotyping.
"Our focus is on targeting those communities where offences of FGM are prevalent, by engaging with passengers travelling to and from countries where the offence is practised.
"We hope to educate and prevent anyone who may engage in FGM; as well as highlighting the support available to those who may be at risk."
There has only ever been one, unsuccessful, prosecution for the practice in the UK, and three more cases are being reviewed by lawyers.
Mr Balhatchet said prosecutions were "far from being the main part of the strategy" to tackle FGM.
Chief executive of children's charity Barnardo's, Javed Khan, said the health figures were "the tip of the iceberg".
"There are likely to be many more women and girls who are living with the harmful physical and emotional consequences of this outdated practice here in England," he said.
"A lack of knowledge and confidence among professionals has stalled successful prosecutions for too long."
So far 13 prevention orders have been made to stop girls being taken abroad to undergo FGM.
The Met said it had dealt with an increasing number of cases, rising from 29 reports in 2012 to 196 in the year to March 2016.
Families with children have been stopped at Heathrow Airport as part of a crackdown on Female Genital Mutilation (FGM).