US Secretary of State John Kerry arrived in Turkey Sunday to discuss Syria's civil war and the Middle East peace process as well as to bolster the Turkish-Israeli rapprochement brokered two weeks ago by Washington.

The top US diplomat was due to meet later Sunday with Turkish Foreign Minister Ahmet Davutoglu and Prime Minister Recep Tayyip Erdogan, before travelling to Israel and the West Bank.

He would "encourage Turkey to expeditiously implement its agreement with Israel and fully normalise their relationship to allow for deeper cooperation," a top State Department official said, asking to remain anonymous.

Such cooperation is seen as important in the Arab-Israeli peace process.

Israel apologised to Ankara on March 22 for the deaths of nine Turkish activists in a botched raid by Israeli commandos on a Gaza-bound aid ship, in a breakthrough engineered by US President Barack Obama during a visit to Jerusalem.

The apology ended a nearly three-year rift between Israel and Turkey -- two key US allies in the region -- and the two countries are due to begin talks on compensation on April 12.

But they have yet to exchange ambassadors and fully restore diplomatic ties, and the US official stressed this "was a pivotal time to encourage them to keep moving forward."

Erdogan accepted the apology "in the name of the Turkish people" but said the country's future relationship with Israel including the return of ambassadors would depend on the Jewish state.

Kerry last visited Turkey on March 1 amid a row over comments by Erdogan branding Zionism a "crime against humanity", remarks the Turkish premier later said had been misunderstood.

In Ankara, Kerry had expressed Washington's hopes to see the two allies reconcile and work together.

Syria will also loom large in their talks, with Turkey having kept its borders open to refugees fleeing the conflict now in its third year.

Turkey, once a close ally of Syria, has joined the United States in its campaign to oust the regime of President Bashar al-Assad and has given shelter to Syrian rebels and to some 200,000 refugees accommodated in several camps along its volatile border.

The huge flows are placing a massive burden on Turkish resources, and Kerry would stress the need to keep the borders open as well as their shared support for the Syrian opposition council, the official said.

After talks in Turkey, Kerry heads later Sunday to Israel and Ramallah in the West Bank, where he will meet with Palestinian president Mahmud Abbas.

He will also meet with Israeli Prime Minister Benjamin Netanyahu on Monday, in what will be his third trip to the Middle East region since the start of his tenure on February 1.

US officials have said the return visit will give him a chance to probe possibilities for restarting the moribund peace process in the wake of Obama's trip last month.

The Turkish-Israeli rapprochement could enable Ankara to play a role in the Middle East peace process and in particular helping reconciliation between rival Palestinian factions, Hamas and al-Fatah, analysts say.

Turkey's Davutoglu held telephone conversations late Saturday with Abbas and Khaled Meshaal, the re-elected head of the Islamist Hamas movement for discussions on steps to be taken for reconciliation between the two parties, the state-run Anatolia news agency reported.

And Erdogan is expected to visit the United States for talks with Obama on May 16.

Kerry's departure for Istanbul was delayed by about three hours when a door on his Boeing 757 malfunctioned, and he was visibly saddened by the tragedy in Afghanistan as he waited with his wife Teresa Heinz Kerry for a second plane to be prepared.

Before leaving, he phoned the parents of a State Department employee who was killed in an Afghan bombing, to offer his condolences. Four other State Department staff were injured, one critically, in the attack.

The US foreign service employee, whom Kerry met late last month when he visited Kabul, died Saturday in a roadside bombing attack of a NATO convoy in Zabul province which killed three NATO troops and two civilians.

"Our State Department family is grieving over the loss of one of our own, an exceptional young Foreign Service officer," Kerry said in a heartfelt statement, condemning the bombing as "a despicable attack."