"The city of Aleppo has been subject to a collective punishment and immoral siege by the armed terrorist groups," Xinhua quoted the ministry as saying in letters addressing the UN.
These groups have cut off the water supplies, including "the clean and drinkable ones, to three million people in the city due to their rejection of the presence of the armed terrorist groups and their crimes against the civilians", it added.
The radical groups, who are in control of two main water pumping stations in Aleppo, have managed to cut off drinking water to the government-controlled western part of the city.
The move that has also rebounded against the rebel-held part of Aleppo, creating a shortage in the rebels' own strongholds.
"The terrorists have prevented the pumping of water through Suleiman al-Halabi station, main source of drinking water in Aleppo, causing a water outage in the whole city for the ninth consecutive day, sending water to Quiq River and wasting it to prevent citizens from having clean water," the ministry said.
While emphasizing that the rebels' action has created a "big dilemma" for people of Aleppo, the statement stressed that the Syrian government and competent authorities are exerting huge efforts to cover people's demands of water by all means and through "urgent solutions".
Aleppo, Syria's largest city and economic hub, has emerged as a main battlefield in the country's three-year crisis since the rebels vowed to "liberate" Aleppo from the government forces in June 2012.
During the long-standing crisis, the rebels have repeatedly attacked the country's infrastructure, plunging large areas in complete power outages and cutting off water to many areas as well.
The three-year crisis started in mid-March 2011 when anti- government protesters took to the street calling for reforms, but rapidly evolved into a civil war.