In a news conference following a Council of Ministers meeting in Ankara on Monday, Yildirim said: "We want to clearly express that these attacks against civilians were not approved."
"The normalization of our relations with Israel will never prevent, stop our stand for Palestinians' justified cases and our common action with them," added Yildirim.
Israeli warplanes launched airstrikes in the blockaded Gaza Strip on Sunday, shortly after a rocket was fired into southern Israel.
On Sunday, the Israeli military said in a statement that a rocket hit the southern city of Sderot from the Palestinian territory.
"In response to the attack, the Israeli air forces and armored corps targeted two Hamas posts in southern Gaza Strip,” the statement said.
Relations with Egypt
Yildirim also said that he looked to improve relations between Turkey and Egypt.
"We are on the side of improving our relations with Egypt," said Yildirim.
"Egypt is a country whose culture, values are close to us, our people are brothers," said Yildirim, adding that the conflicts between governments should not be reflected on the people.
Yildirim's remarks came after Egyptian President Abdel-Fattah al-Sisi's statements on Sunday.
“There is no reason for animosity,” al-Sisi said in statements to Egypt’s three pro-government newspapers Sunday. “We gave them [Turkey] the time to reconsider their position,” he said.
Turkish-Egyptian relations deteriorated after the army led by al-Sisi ousted Mohamed Morsi, the country’s first freely elected president, in a 2013 coup.
Bloodshed in Syria
The Turkish prime minister also addressed the Syrian crisis.
"Syria is, unfortunately, losing its energy day by day with a civil war that has gone on for six years."
Yildirim said that millions of people have been displaced across the war-battered country, and around 500,000 people lost their lives since early 2011.
"It is essential in Syria to stop the bloodshed by the coming together of all parties and to form an administration representative of all Syrians," added Yildirim.
Yildirim summarized Turkey's position on Syria's future to three main positions: "Non-division of Syria, preservation of its territorial integrity, and the disallowance of a new reconstruction that provides an advantage to an ethnic group."
Syria has been locked in a vicious civil war since early 2011, when the Bashar al-Assad regime cracked down on pro-democracy protests -- which erupted as part of the "Arab Spring" uprisings -- with unexpected ferocity.
Since then, more than a quarter of a million people have been killed and more than 10 million displaced across the country, according to the UN.
The Syrian Center for Policy Research, however, put the death toll from the six-year conflict at more than 470,000 people.