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"We were informed by the Formula One authorities yesterday. Obviously we feel it is a great pity," Suzuka's public relations chief Yasuo Sugaya told Reuters.
"But we are continuing negotiations in order to be included from the 2008 season."
Suzuka, Honda's home circuit, stages its 20th Formula One race on October 8 before Fuji Speedway takes over the Japanese Grand Prix next year.
Toyota-owned Fuji had already been confirmed for the 2007 race but Suzuka officials were hoping another Pacific round could be included for them to host.
"We had been hopeful we could come to an arrangement to have two races but unfortunately it was not to be," said Sugaya. "It's still possible we can come back next year (2008) so we'll keep trying."
Japan held two races in the 1994 and 1995 seasons when the remote Aida circuit staged a Pacific Grand Prix.
Fuji, built in 1966, hosted the first grand prix in Japan in 1976, when James Hunt finished third in a rainstorm to clinch the world title.
The Briton also won the second race in 1977 but his joy was overshadowed by a crash which killed two people at trackside and there was no Japanese Grand Prix for the next 10 years.