Tests on rats by US doctors showed that the offspring of those exposed to moderate to high doses of alcohol had a higher number of breast tumours than other animals.
A separate study has found that the effects of maternal drinking on babies continues into adolescence.
Children with foetal alcohol syndrome commonly have growth defects.
But research published in the journal Alcohol: Clinical and Experimental Research found the effect could still be detected in 14-year-olds.
Oestrogen levels
The research into breast cancer risk was carried out after earlier studies showed a mother's diet during pregnancy could affect her daughter's future breast cancer risk.
The theory is that diet can increase oestrogen levels and that high levels in the womb increase breast cancer risk by making the developing breast cells vulnerable to later events that can turn them malignant.
Alcohol increases both oestrogens in the blood and breast cancer risk, the researchers add.
Rats were either given moderate and high amounts of alcohol or no alcohol at all during pregnancy.
Alcohol appeared to increase oestrogen levels in the pregnant rats, but researchers saw no adverse effects on foetal development.
When the female offspring reached adulthood, they were given a carcinogen to initiate breast cancer.
Those who were exposed to a moderate or high dose of alcohol while in the womb had a significantly higher number of breast tumours when compared to those who had not been exposed to alcohol.
Breast cancer risk
The researchers say that although there are no comparable human studies available, there is evidence that alcohol intake increases pregnancy oestrogen levels in women.
They add that other research has shown that what happens to a baby in the womb influences future breast cancer risk.
Anna Cabanes, of the Department of Oncology, Lombardi Cancer Center at Georgetown University, who worked on the study, said: "Women should continue to heed warnings that alcohol intake during pregnancy should be significantly limited to protect their offspring."
The research was presented to the Frontiers in Cancer Prevention Research meeting held in Boston by the American Association for Cancer Research.