"The launching of premature Israeli threats against Syria lacks the least degrees of credibility or evidence," the official SANA news agency quoted Foreign Minister Faruq al-Shara as saying on Thursday.
Al-Shara added that the threats "exacerbate the deteriorating situation in the region."
Israeli security officials have said its military would respond to Tuesday's twin bus bombings - the first such attacks inside the mainly Jewish state in nearly six months.
The officials warned Israeli forces would pursue a renewed assassination campaign against leaders of Hamas, the armed resistance group behind the attacks, in both the Palestinian territories and abroad.
Israel's threats have heightened regional tensions by raising the spectre of an air raid similar to the one carried out deep inside Syria in October 2003 against an alleged Palestinian training camp.
Damascus defends armed Palestinian groups as legitimate resistance to Israeli occupation despite US and Israeli pressure to expel those groups' leaders.
Hamas has denied that its leadership outside the Palestinian territories was involved in Tuesday's attacks.
Hamas political chief Khalid Mishaal, who survived an Israeli assassination attempt in Jordan in 1997, is based in Damascus.