The 25-year-old Halima Cisse gave birth to the babies via Caesarean section on Tuesday in Morocco after being sent there for special care, the ministry announced.
"The newborns (five girls and four boys) and the mother are all doing well," Mali's health minister said in a statement.
Cisse had been expecting seven babies.
Malian doctors, under government orders, sent Cisse to Morocco for the births because there wasn't adequate equipment to deal with this extremely rare pregnancy.
The private Ain Borja clinic in Casablanca, where she was treated, confirmed she gave birth there.
CNN reports that multiple births are rare. In the U.S., 87.7 per 100,000 live births were of triplets or more, according to 2019 data from the CDC.
The record for the most children delivered at a single birth to survive belongs to Nadya Suleman, who in 2009 gave birth to six boys and two girls in California, according to the Guinness World Records.