The warning comes as tension grips Lebanon fueled by political instability and conflict in neighboring Syria.
The ministry said local authorities were taking all necessary steps to provide security to Turkish citizens and Turkish companies in Lebanon.
However, the ministry still requested Turkish citizens in Lebanon to follow warnings and advice of their Turkish embassy.
There have been several clashes between the Lebanese army and various armed groups in the country, including those affiliated with the Islamic State of Iraq and the Levant.
Several Lebanese army personnel were captured in early September during clashes with militant groups in Arsal on the border with Syria.
The clashes erupted after Lebanese authorities arrested some Sunni figures said to be close to or associated with militant groups fighting against the regime of Syrian President Bashar al-Assad and allied troops from the Shiite Lebanese Hezbollah group.
According to the UN Refugee Agency, the impact of the Syrian crisis, including on the economy, demographics, political instability, and security, continues to deepen across Lebanon.
“With more than 1.3 million refugees expected by the beginning of 2015, Lebanon's exceptional hospitality will be extremely stretched,” the agency said.