Foreign Minister Walid Muallem issued the threat on Syrian state media after his team held talks with UN negotiator Lakhdar Brahimi.
Lakhdar Brahimi is due to meet the Syrian opposition separately later on Friday.
Correspondents say the talks have been troubled from the start, as both sides have deeply entrenched positions.
Syria’s civil conflict has claimed well over 100,000 lives, the UN says.
The violence has also driven 9.5 million people from their homes, creating a major humanitarian crisis within Syria and for its neighbors.
Fighting continued on the ground on Friday, with government forces bombing rebel-held areas in the northern city of Aleppo, according to the British-based Syrian Observatory for Human Rights.
This is the third day of the Geneva conference, but the first in which negotiations get under way in earnest.
There were initial hopes of a joint meeting between the two sides, but later it emerged that Mr Brahimi would hold talks with each separately.
Both sides blame the other for this setback.
The Damascus delegation complained about recent remarks made by the opposition chief, Ahmed Jarba, who said President Bashar al-Assad and his regime were a “political corpse” that could not be part of Syria’s future.
For its part, the opposition said it would not meet government delegates face-to-face until they signed a written commitment accepting the Geneva communiqué drafted 18 months ago, which calls for a transitional government.
While the two sides are opposed on many issues, they have both indicated a willingness to talk about concrete steps like local ceasefires, prisoner exchanges and establishing safe corridors for the delivery of badly needed humanitarian aid.
One of the main sticking points between the government and the rebels is the role of Bashar al-Assad.
The opposition demands his removal from office as a condition for peace.
It is supported in this by many key foreign observers, including Secretary of State John Kerry.
Syrian officials have flatly rejected any suggestion of Bashar al-Assad stepping down, and he has even suggested he will run for president again in elections due this year.
The Syrian government also has its supporters: Russia’s Deputy PM Arkady Dvorkovich.
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