Ask for a conference with your daughter's teacher, the gym teacher, and the school counselor. Explain what you are seeing with your daughter and what she has told you about being afraid. Work out a plan with the three staff members as to what will happen on gym days.
Perhaps the classroom teacher or the counselor could sit with your daughter on the sidelines for the first ten minutes of gym time until she is comfortable, and then your daughter could join the class. Perhaps the gym teacher could meet with your daughter and the counselor and explain what happens in gym class and why most children believe it is fun.
Whatever the three of you work out, reassure your daughter that the adults understand her feelings and want to help her feel happy about going to gym class. With some patience and understanding, your daughter should get over this fear fairly quickly.