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According to Donald H. Akenson (p. 146), it was suppressed by the later Rabbis.
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The rabbis of the first centuries A.C. had mixed opinions regarding apocryphical books (״ספרים חיצוניים״). Though some maintained that these books were holy (though not to be read by laymen), others claimed that the reading of these books was enough to condemn one as a heretic.
The Book of Jubilees may have been especially suppressed as it espoused a solar based calendar, in contrast to the dominant view supported by the Pharisees, according to which the months are lunar based.