According to the BBC, archaeologists fear that the 2,600-year-old Buddhist monastery, complete with domed shrines known as stupas, would probably be largely destroyed once work at the mine begins.
The site is located at Mes Aynak, in the eastern province of Logar.
The mine is reportedly the centrepiece of China's drive to invest in Afghanistan, as Kabul tries to re-energise an economy still blighted by the ongoing war.
Beijing's 3.5 billion dollars stake in the mine is believed to be one of the largest foreign investments in Afghanistan by far, and means that China has a head start when it comes to negotiating future deals to exploit the country's largely untapped mineral wealth, including iron, gold and cobalt. The Afghan government stands to reap a potential 1.2 billion (755 million pounds) a year in revenue from the mine, as well as create much-needed jobs, the report said.
The ruins were discovered as labourers excavated the site on behalf of the Chinese government-backed China Metallurgical Group Corp (MGC).
Hanging over the discovery is the memory of the Buddhas of Bamiyan, Buddhist statues towering up to 180 feet (54.86 metre) high in central Afghanistan that were dynamited in 2001 by the Taliban, who considered them symbols of paganism, the report added.
Since nobody wants to be blamed for similarly razing history at Mes Aynak, an informal understanding between MGC and the Afghan government was reached, which initially gave archaeologists three years for a salvage excavation.
"The site is so massive that it's easily a 10-year campaign of archaeology. Three years may be just enough time only to document what's here," US archaeologist Laura Tedesco said.
About 15 Afghan archaeologists, three French advisers and 24 labourers are working at the site, a far smaller team than is normally needed.
The monastery complex has been dug out, revealing hallways and rooms decorated with frescoes and filled with clay and stone statues of standing and reclining Buddhas, some as high as 10ft (3m). Over 150 statues have been found so far. (ANI)