The research will likely do little to help simmering hostilities between the Asian giants, a relationship marred by historical animosities and territorial disputes.
"Whenever readings were high, winds were blowing from the continent (China)," Osamu Nagafuchi, the lead scientist on the study, told AFP on Thursday.
Fuji was chosen "because it's a place unaffected by urban pollution", said Nagafuchi, an environmental science professor at the University of Shiga Prefecture.
Pollution levels on Mt. Fuji have been monitored annually since 2007, he said, adding the decision to carry out the study on the 3,776-metre (12,389-feet) peak had nothing to do with it being designated a UNESCO World Heritage site earlier this year.
The UNESCO designation led to a surge in visitors to the iconic peak -- which figures heavily in Japanese art and literature -- during this summer's climbing season.
Mercury levels around the top of peak were up to double levels found in other places free of heavy pollution, according to the survey, conducted in August with non-profit group Valid Utilization of Mt. Fuji Weather Station.
The levels were as high as 2.8 nanogrammes of mercury in one cubic metre of air.
That is above levels around 1.0 to 1.5 nanogrammes normally detected in clean places, but still below the 40 nanogramme government threshold for posing risks to human health. A nanogramme is one billionth of a gramme.
The higher-than-expected readings are likely due to Chinese factories burning coal, which releases mercury and other toxic elements -- such as arsenic -- which were also elevated, Nagafuchi said.
The study comes as fast-industrialising China wrestles with a severe urban air pollution problem linked to hundreds of thousands of premature deaths.
Last month, China vowed to reduce levels of atmospheric pollutants in Beijing and other major cities by as much as 25 percent to try to improve their dire air quality.
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