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First and foremost, the Saffir-Simpson scale is used to rate hurricanes while the Fujita scale is used to rate tornadoes.

The Saffir-Simpson scale is based on direct wind measurements, with the winds for each category generally being lower than those of the "equivalent" levels on the Fujita Scale (now the Enhanced Fujita scale in the U.S.), for example, a category 5 Hurricane starts at 156 mph while an F5 tornado starts at 261 mph (201 mph for an EF5). Furthermore, the (Enhanced) Fujita scale bases ratings on damage rather than direct wind measurements, with the winds being estimates.

These differences are dues to the fact that tornadoes are much smaller and shorter-lived than hurricanes, making it very difficult or even impossible to get direct wind measurements.

The winds for the (E)F scale categories are higher than those on the Saffir-Simpson scale largely because tornadoes can have much faster winds: tornadoes can have winds over 300 mph, while the very strongest of hurricanes have winds of about 200 mph.

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Q: Why do the saffir-Simpson scale and fujita scale differ?
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Theodore Fujita develop the fujita scale in 1971


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