Babacan also repeated Turkey's assertions that Ankara had no prior knowledge of the September 6 air raid by Israel.
"I hope that during my visit to Israel to be given answers and clarifications about this issue," Babacan said.
"The region is at a very dangerous and sensitive stage. We always urge all parties to reach solutions through dialogue and peaceful means."
Israel confirmed this month that it had carried out an air attack on Syria, but both countries have revealed little information on the target of the air raid.
Diplomats said at least four Israeli jets flew in attack formation along the Syrian-Turkish border before striking deep into Syria.
Al-Assad has said the raid targeted an unused building linked to the Syrian military.
Ankara and Damascus have built closer security and economic ties in recent years, despite persisting water disputes and past Syrian support for Kurdish rebels.
Turkey, a member of Nato, also has good ties with Israel and allows Israeli jets to train on its territory, according to diplomats in Damascus.
The air attack came after speculation that Syria and Israel, which remain formally at war, could resume peace talks that collapsed in 2000.