Yes, medication abortion and emergency contraception are different.
The use of emergency contraception does not cause an abortion. In
fact, emergency contraception prevents pregnancy and thereby reduces a
woman's need for an abortion.
Medical science defines the beginning of pregnancy as the implantation
of a fertilized egg in the lining of a woman's uterus. Implantation
begins five to seven days after fertilization (and is completed several
days later). Emergency contraceptives work before implantation and
not after a woman is already pregnant. If a woman takes emergency contraception
when she is already pregnant, emergency contraception will not
interfere with the established pregnancy and it is not teratogenic. More information
on emergency contraception can be obtained at www.not-2-late.com.
This site is available in English, French, Spanish, and Arabic.
Medication abortion works by terminating an existing pregnancy. Thus,
medication abortion only works after fertilization and implantation
Reference:  Finer
L, Henshaw S. Abortion Incidence and Services in the United States
in 2000. Perspectives on Sexual and Reproductive Health. 2003; 35(1):