A Chinese construction company has severely damaged relics dating back more than 3,000 years while building a section of a high-speed rail linking Beijing and Shanghai, state media says.

Work was halted on the section of rail in the eastern city of Nanjing and the company faces a fine of up to 500,000 yuan (AU$80,000) for ignoring warnings that the site contained ancient treasures, the China Daily said.

"These precious cultural relics absolutely must be excavated before construction continues," Nanjing's Cultural Heritage Bureau deputy director Yang Qinghua was quoted as saying.

"You can't just ignore them."

Nearly 2,000 square metres of the site was damaged last week when the company shrugged off experts' instructions not to work on the area in China's ancient capital, Yang was quoted as saying.

The incident is the latest battle between those seeking to drive China's explosive growth forward at any cost and those wanting to preserve the country's priceless historical heritage.

The site was identified in October after bones and pottery dating back to the Shang Dynasty (16th to 11th century BC) and the Zhou Dynasty (11th to 3rd century BC) were discovered there, Yang said, according to the report.

Heritage officials initially told the company it would have to redirect the rail line, but company officials refused, saying the project was of national importance, Yang was quoted as saying.