That master plan, designed by Daniel Libeskind and David Childs, features a 1,776-foot "Freedom Tower" and a 4.5-acre area for a memorial to 9/11 victims.
But Trump told reporters at a news conference: "Throw it all away."
The Lower Manhattan Development Corp. reported that the agency will continue to move forward with the master site plan.
Already, the cornerstone for the Freedom Tower has been laid on the site, though earlier this month New York Gov. George Pataki announced that the iconic tower would be tweaked to accommodate security concerns raised by the New York Police Department. A revised tower design is to be unveiled next month.
The Freedom Tower design was chosen in February 2003 after some of the world's best-known architects submitted proposals. Its height is symbolic of the year of American independence, and its 276-foot spire is meant to echo the arm of the Statue of Liberty.
The torqued glass-and-steel design includes a steel cable netting, more than 60 floors for offices, an indoor observation deck, a restaurant and wind-harvesting turbines to supply some of the building's power.
Trump made it clear he doesn't like it, saying that the plan "looks like a junkyard."
Trump's alternative would be replicas of the original 110-story towers, only a bit taller. The design and model by architect Ken Gardner, embraced by Trump, offered buildings that would be 1,474 feet — more than a hundred feet taller than the original towers, once the world's tallest buildings.
Trump's plan would also mean scrapping the memorial plaza that was also chosen after an international design competition.
In a written statement sent to CNN, Libeskind said, "The site plan is not just about commercial buildings. The memorial is its crucial centerpiece. It is there for a reason. The museums are there for a reason. The performing art center is there for a reason. The public open space is there for a reason. The transportation hub is there for a reason. "Together they reflect the rich tapestry of our national spirit. They respond to the loss of 3,000 lives on this sacred ground but also reaffirm with optimism and determination of our democratic values and the true American dream. "The master plan provides a context for these elements to coexist as a forceful, coherent and enduring whole -- both respectful of history and also defiantly alive."
Trump said he hoped that World Trade Center leaseholder Larry Silverstein, who is slated to construct the Freedom Tower, would get behind his plan.
But Silverstein indicated otherwise, saying his "only concern right now is designing a safe and spectacular Freedom Tower in keeping with the well-established master plan for the site."
Silverstein already has $4 billion in insurance proceeds and the backing of the state's political establishment, led by Pataki.
Trump is responsible for a number of tall apartment and office buildings around Manhattan -- all with his name emblazoned on them. They include his headquarters, 5th Avenue's Trump Tower, and the tallest residential building in North America, Trump World Tower, which rises 861 feet across the street from the United Nations.
