The decision threatens the process sponsored by regime ally Russia and rebel backer Turkey, which began with a truce and is meant to lead to negotiations in the Kazakh capital Astana this month.
The ceasefire has brought quiet to large parts of the country but has been undermined by sporadic violence, particularly fighting in the Wadi Barada region north of Damascus.
The area is the main water source for the capital.
Government forces backed by fighters from Lebanon's Hezbollah group have continued to press a two-week-old offensive despite the ceasefire which began December 30.
A dozen rebel groups said in a statement late Monday that they were withdrawing from talks to prepare for the new round of negotiations in Astana.
"As these violations are continuing, the rebel factions announce... the freezing of all discussion linked to the Astana negotiations," they said.
The rebels said they "respected the ceasefire across the whole of Syria... but the regime and its allies have not stopped shooting and have launched major and frequent violations, notably in the (rebel) regions of Wadi Barada and Eastern Ghouta", near Damascus.
"If things don't return to how they were before, the accord will be considered null and void," the statement added.
It was signed by a dozen groups, including the Army of Islam, Faylaq al-Sham, and the Sultan Murad Brigade, which is close to Turkey.
- 'Critical phase' -
The fighting in Wadi Barada continued on Tuesday, the Britain-based Syrian Observatory for Human Rights monitor said.
The group said government forces were attacking with helicopters and artillery fire after advancing on Monday to the outskirts of the Ain al-Fijeh spring, the main water source in the area.
Syria's government accuses rebels in Wadi Barada of deliberately targeting infrastructure there, causing fuel to poison the water supply and then cutting the flow to Damascus altogether.
Rebels say government strikes caused the damage, which has left four million people in Damascus without water since December 22.
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The regime says forces in Wadi Barada include former Al-Qaeda affiliate Fateh al-Sham Front, although opposition fighters deny the group is present.
Fateh al-Sham, along with the Islamic State group, is excluded from the truce.
Observatory director Rami Abdel Rahman warned the truce was in a "critical phase" and faced the prospect of "collapse" if sponsors Russia and Turkey did not intervene to save it.
The monitor reported violations elsewhere in the country on Tuesday, including air strikes on the town of Khan Sheikhun in Idlib province that killed a pregnant woman and wounded three other civilians.
The group also reported rebel fire on two villages in the central Hama province.
- Spillover in Turkey -
The ceasefire and planned talks are the latest effort to negotiate an end to Syria's conflict, which has killed more than 310,000 people since it began with anti-government protests in March 2011.
Despite backing opposite sides in the conflict, Ankara and Moscow have worked closely of late on the war, jointly brokering a deal that allowed civilians and rebels to leave Aleppo city before it was retaken by the government last month.
The process has also received the blessing of the UN Security Council, despite offering a competing track to UN-sponsored negotiations set to resume in Geneva in February.
Russia and Turkey, which are organising the talks along with regime ally Iran, say they are meant to supplement the UN-backed process, not replace it.
Both Russia and Turkey have launched their own military action in Syria, with Moscow intervening in support of the government in September 2015, and Ankara starting a campaign against the Islamic State group and Kurdish militants in August 2016.
The conflict has spilled into Turkey, with a string of deadly attacks claimed by or blamed on IS or Kurdish groups.
On Monday, IS claimed responsibility for a New Year's night attack on an Istanbul nightclub that killed 39 people.
Turkey's Hurriyet daily reported Tuesday that the attacker, who remains at large, had fought for IS in Syria.