"Our role is changing in Africa because the world is changing in Africa, because public opinion is changing, because governments are changing," he said.
Macron was addressing French forces stationed at the strategic Horn of Africa nation before sitting down for a Christmas meal with the troops, a regular feature on the presidential calendar.
France had to change its past logic of having too many military bases in Africa, he said.
In recent years, Mali, Burkina Faso and Niger, all three under military rule, have told France to get its troops out.
They have turned instead to Russia for military support in their fight against the jihadist forces active in the region.
And on Friday, France also began withdrawing ground troops from Chad, after N'Djamena last month abruptly ended military cooperation with the former colonial power.
The central African country was the last Sahel nation to host French troops.
Its decision also came shortly after Senegal's President Bassirou Diomaye Faye told AFP in an interview that France should close its military bases there.
Djibouti has in the past been part of France's Indo-Pacific strategy, contributing to freedom of navigation in the Red Sea.
"It is also, and will also have to be reinvented as, a projection point for some of our African missions," Macron said, without elaborating.
The French base at Djibouti currently hosts 1,500 soldiers.
That makes it France's largest military contingent abroad and the only one untouched by the military draw-down African nations have imposed on Paris.
In July, Djibouti and France renewed their defence cooperation treaty.
As well as paying rent for the base, France also assumes responsibility for patrolling the airspace over the country.
The small east African state is a relative haven of stability. On the other side of the Red Sea lies Yemen, gripped in a devastating civil war.
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