John Marburger said that the support voiced by Washington for the northern Japanese village of Rokkasho-mura was based on a preliminary assessment of the site by the US Department of Energy.
Partners involved in the project were now seeking detailed technical information about the rival bids to try to break a negotiation deadlock, Marburger told reporters.
Asked whether that meant the Department of Energy might switch its recommendation to Bush, Marburger said, "It could change."
"There has been a lack of understanding about the nature of this process," Marburger said, referring to a perception that US backing for Rokkasho-mura was set and final.
"In the process of negotiating the position of this site, clearly you have to put your position on the table. ...
"As more knowledge becames available, we expect our representatives from the Department of Energy to analyse it and if they come to a different conclusion, then I expect them to make a recommendation to the president based on the facts as they see them," Marburger said.
ITER, or the International Thermonuclear Experimental Reactor, aims to test technology for nuclear fusion, billed as the clean, safe, inexhaustible energy source of the future.
The European Union, the United States, China, Japan, South Korea and Russia are to vote in late February on whether the southern French town of Cadarache or Rokkasho-mura should host the 10 billion dollar project.
They failed to decide on the site at a meeting in December, with Japan drawing backing from the United States and South Korea, while France won support from China and Russia.
Marburger said among the technical details that were being solicited for the February meeting were transport access and the sites' seismic profiles.
He was speaking at the start of a two-day meeting of science and technology ministers from the Organisation for Economic Cooperation and Development (OECD).