Two officials say the girls were admitted to Panzi Hospital in South Kivu province over the past two months with serious internal wounds.
U.N. special representative to Congo Roger Meece and UNICEF representative Barbara Bentein released their statement through U.N. deputy spokesman Eduardo del Buey on Thursday.
The officials said two suspects have been arrested, but they urged Congolese authorities to follow through with the "prosecution of all perpetrators involved in this despicable practice."
The U.N. has said various armed groups are behind rapes in eastern Congo. The Congolese army and M23 rebels also have been accused of rapes.