The Kenyan-born Shahin, formerly known as Stephen Cherono, has not received permission from the Kenyan Olympic Committee to be able to compete at the Olympics for Qatar.
"Unfortunately I will not be able to start in the Olympic Games this summer," he said after finishing fifth in the world cross country short race on Saturday.
The International Association of Athletics Federations (IAFF) is considering a change in rules to prevent athletes from switching countries for commercial gain, but will not have new laws in time for Athens.
Under the current rules, three years must pass before an athlete can compete for another country, unless there is a bilateral agreement to skip the measure. Kenya said it would refuse to allow Shahin to run in Athens.
Shahin said Qatar agreed to pay him $1000 a month for the rest of his life to make the switch of allegiance. He was allowed to compete at the world track and field championships last year, and became the first non-Kenyan to win the steeplechase in 16 years.
Kenya also suffered from the drain of athletes to Qatar at the cross country championships. It missed out on the team gold medal in the short race for the first time to Ethiopia, and was even pushed into third place by Qatar, which has several former Kenyans on its team.
"Unfortunately I will not be able to start in the Olympic Games this summer"
Saif Said Shahin,
Shahin knows the nationality switch problem has affected several athletes at the Olympics in the past.
Kenyan-born Wilson Kipketer was barred from running the 800m for Denmark at the 1996 Atlanta Olympics, forfeiting an almost certain gold medal. Cuban-born long jumper Niurka Montalvo was barred by Cuba from competing at the 2000 Sydney games for Spain.
Shahin was further disappointed by his fifth-place showing at the world cross country championships, held in driving rain and winds.
"It was a disastrous race," he said. "I felt like being stuck in the mud all the time."