In a letter sent to the UN to complain about the terrorists' crimes in the country, the ministry said the Nusra Front and the so-called Islam Brigade carried out a new massacre last Wednesday in the Adra Umalyeih suburb of Damascus, Xinhua reported.
It further added that the hard-liners had burnt the houses of the state servants in the area and took a large number of civilians as human shields.
The ministry lambasted Arab news outlets that offer a media cover for the terrorists, saying those outlets financed by Saudi Arabia and Qatar are inciting sedition and killings in Syria.
It said that radical rebels from more than 80 countries are pouring into Syria, urging the UN member states to denounce the terrorism that Syria is subject to.
The Syrian army started Friday a wide-scale offensive against the radical rebels in Adra, media reported citing a military source.
The large-scale military operation aims at dislodging the Al Qaeda-linked Nusra Front fighters from Adra, a couple of days after the fighters stormed the town, killing tens of people.
The Nusra has also slaughtered people from the Alawite minority in Adra and placed their heads in the most popular market in the town.
"Unites of our military forces have started storming the rebels' positions in Adra," the Syrian military source said.
The source added that "the criminals and those who support them will pay a steep price for the crimes they are committing against our people."
Al Qaeda-linked groups such as the Nusra Front and the Islamic State of the Iraq and the Levant have taken advantage of the anti-government movement in Syria, emerging as a serious force among the rebel groups.
The radical rebels stormed Adra following their defeat in three major towns in the rugged al-Qalamoun region north of Damascus, namely al-Nabek, Deir Attieh and Qara.