Marlene Schiappa, who is in charge of citizenship in France’s government, said the teenager was found on the beach of Sangatte on Wednesday morning.
The tragedy comes as migrants making the perilous crossing of the English Channel has been a focus of the UK Government amid a record number of journeys.
Immense tristesse: un adolescent de 16 ans, migrant soudanais disparu en mer cette nuit, a été retrouvé mort sur la plage de Sangatte ce matin.
Ce drame insupportable nous mobilise encore + avec @GDarmanin contre les passeurs qui profitent de la détresse d’êtres humains !— 🇫🇷 MarleneSchiappa (@MarleneSchiappa) August 19, 2020
The UK's home secretary Priti Patel, who has pledged to make the route “unviable”, said the death is “an upsetting and tragic loss of a young life”.
“This horrendous incident serves as a brutal reminder of the abhorrent criminal gangs and people smugglers who exploit vulnerable people,” she added.
“Working together we are determined to stop them.”
Ms Shiappa also said the death highlighted the need to tackle the smugglers.
“Immense sadness: A 16-year-old Sudanese migrant who disappeared in the sea last night was found dead in the beach in Sangatte this morning,” she tweeted.
Meanwhile in Dover children were among dozens of migrants who arrived on Wednesday morning.
More than 50 people were taken into the Kent port on Wednesday morning aboard a lifeboat and a Border Force vessel.
The fresh arrivals came amid urgent discussions on where to house migrant children who travel to the UK without family.
It emerged earlier in the week that any new, unaccompanied asylum-seeking children would be left with Border Force after Kent County Council announced it had reached capacity.