Premier Li Keqiang expressed his regret to Mexican President Enrique Pena Nieto, who was in Beijing to attend the two-day Asia-Pacific Economic Cooperation (APEC) meeting.
He asked the Mexican government to "fairly" treat Chinese enterprises investing in the country, state-run Xinhua news agency reported.
The China Railway Construction Corporation (CRCC), which was awarded the contact in a sing bid auction, has said it is "extremely shocked" by Mexico's decision to withdraw the deal and pledged to resort to legal means to protect its interests.
A consortium of Chinese and Mexican companies led by the CRCC had won the bid to build a 210-kilometre-long high-speed railway connecting Mexico City with the industrial hub of Queretaro to the north.
Mexico's Ministry of Communications and Transport has said Nieto's decision to scrap the deal was aimed at clearing any public doubts about the project.
The CRCC has stressed that the firm has strictly followed the bidding procedures and requirements, and the bidding content complied with the requirements of the Mexican government.
Construction of the rail line, part of Mexico government's plan to boost Latin America's second-biggest economy, was due to start in December, with services running from 2017.
Mexico would become the first Latin American nation to have a bullet train after Brazil and Argentina postponed their own high-speed rail projects.
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