The 25-year-old was arrested at the high-security mission on Sunday after the girl's family complained of the sexual assault, which allegedly took place on Saturday at the living quarters for local housekeeping staff.
"The accused was arrested on Sunday immediately after the parents complained about the sexual attack," investigating officer Yogesh Kumar said.
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Kumar said preliminary medical tests confirmed the girl had been raped. The man was charged under child rape laws that carry the death penalty.
The sprawling diplomatic compound is one of the most secure in Delhi, with multiple layers of manned and electronic security.
India is struggling to combat a growing number of sexual assault cases in the country.
Violence against women in the South Asian nation has been under the international spotlight following the brutal gang-rape and murder of a Delhi student on a bus in 2012.
Almost 34,000 rapes were reported in 2018, according to official data, with activists claiming the figure is just the tip of the iceberg.
Experts said most child victims are known to their abusers, with their families frequently choosing not to report the crimes to authorities amid social taboos against speaking out.
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