The Sri Lankan government said the Chinese investor would be granted new land on a 99-year lease instead of the freehold in the original deal entered into when Chinese President Xi Jinping visited Colombo in 2014.
"The tripartite agreement has many features that are beneficial to Sri Lanka that was lacking in the 2014 agreement that is now being replaced," the government said in a statement.
The Sri Lankan government had put the project on hold pending a review of all the big-ticket agreements signed under the previous administration of Mahinda Rajapakse.
The entire project has also been renamed "Colombo International Financial City" instead of the original title of "Port City" given to the reclamation of 269 hectares of land just next to the main Colombo harbour.
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CCCC said it expected the project to create 83,000 new jobs and help Sri Lanka attract another USD 13 billion in direct foreign investment to develop infrastructure within the reclaimed land.
"India had a big concern about giving freehold land to China near the Colombo harbour," government spokesman Rajitha Senaratne told reporters at the time.
"We have amended the agreement. There will be no freehold land but it will be on a 99-year lease."
Former president Rajapakse relied heavily on Chinese investment to rebuild the country's infrastructure after the end of the island's decades-long ethnic war in May 2009, a move which some say alienated India.
Beijing has been accused of seeking to develop facilities around the Indian Ocean in a "string of pearls" strategy to counter the rise of rival India and secure its own economic interests.
China, the largest single lender to Sri Lanka, secured contracts to build roads, railways and ports under Rajapakse, who is under investigation over allegations of corruption during his decade in power.