"There is no medical reason to abstain completely from alcohol while breastfeeding," Annica Sohlstroem, head of the agency's nutrition department, said in a statement.
"The amount of alcohol that the child can ingest through the breastmilk is small if you drink one or two glasses of wine" per week, she said.
The new advice is an about-face for the agency, which has for the past decade or so advised women to avoid alcohol while breastfeeding, and is based on current medical research.
The recommendation is however still a proposal and will be sent to other government agencies for consideration.
The agency, which aims to monitor food quality sold and produced in Sweden, stressed its intention was not to encourage women to drink while breastfeeding and strongly advised women to continue to abstain from alcohol while pregnant.