The order comes a month after a television report that Ethiopian women immigrating to Israel had been coerced into receiving birth control shots, the Jewish Telegraphic Agency reported Monday.
During the broadcast, Ethiopian women said they received shots of Depo-Provera at Jewish-run health clinics in Ethiopia and after they arrived in Israel.
Health Ministry director-general Ron Gamzu told the clinics in a letter "not to renew prescriptions for Depo-Provera for women of Ethiopian origin if for any reason there is concern that they might not understand the ramifications of the treatment."
The letter was the first acknowledgement by an Israeli official that Ethiopian women in Israel had been administered the drug, the agency reported.
The Ethiopian birth rate has declined 50 percent in Israel over the past decade.
The American Jewish Joint Distribution Committee, which runs the health clinics in Ethiopia, said the injections were purely voluntary.
"At no time did JDC coerce anyone into engaging at family planning at its clinics," a JDC spokesman in New York said in December after the show aired.