Macron is on holiday with his wife Brigitte in the southern port of Marseille, staying in a large state-owned villa in a wealthy residential area in the south of the city.
A presidential spokeswoman said that the photographer had repeatedly followed the couple on his motorbike and ignored requests from Macron's security team to stop.
"On Sunday, he entered the private property (of Macron's villa) which led to the complaint," the spokeswoman added.
Celebrity magazine VSD said he had been detained six hours by police before being released.
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Macron's destination for his first holiday since being elected in May has been closely analysed in the French press.
The 39-year-old leader instructed his government ministers to take their holidays in France, rather than abroad, and himself opted to take only a few days off.
The choice of Marseille, a gritty working-class port, was deliberate instead of the more popular and flashy tourist destinations on the Mediterranean coast like Saint-Tropez, some commentators believe.
In 2007, right-winger Nicolas Sarkozy headed to the United States after his election to spend time with his family at an ultra-luxury home on the edge of a lake in New Hampshire.
The choice helped cement Sarkozy's nickname as the "bling-bling" president who allegedly enjoyed the lifestyle of the rich and famous.