Three Turkish soldiers were "accidentally" killed and 11 wounded on Thursday when a Russian air strike targeting jihadists in Syria hit a building where the troops were deployed, the Turkish army said.

With Moscow and Ankara cooperating ever more closely on Syria, President Vladimir Putin quickly reached out to Turkish counterpart Recep Tayyip Erdogan to express condolences and promise better future coordination.

The Russian plane had been seeking to hit targets of Islamic State (IS) jihadists but "by accident three of our heroic soldiers were martyred when a building was bombed where our units were," the Turkish army said in a statement.

It said that of the 11 injured, one was badly wounded.

Putin contacted Erdogan to express his "sadness and condolences," it added.

"Russian officials have said that the incident was an accident," the army said, adding an investigation is being carried out by both sides.

In Moscow, the Kremlin said Putin had offered Erdogan his condolences and that the leaders had "agreed to enhance military coordination" in the fight against IS in Syria.

It said the incident took place in the flashpoint IS-held town of Al-Bab where both countries have been conducting air strikes.

Kremlin spokesman Dmitry Peskov said the Russian strike took place on Thursday morning due to a "lack of agreement of coordinates during strikes by the Russian air force."

- Fight for Al-Bab -

Both sides appeared keen to move on from the incident, as was the case when an off-duty Turkish policeman shot dead Russia's ambassador to Ankara Andrei Karlov on December 19 in a crime that shocked both countries.

Then, Ankara allowed Russian investigators to work in Turkey and also gave the slain ambassador the honour of a ceremony on the tarmac of Ankara airport before his corpse was airlifted back to Russia.

The Russian defence ministry said Chief of the General Staff Valery Gerasimov and Turkish counterpart Hulusi Akar had in a call "agreed on closer coordination of joint actions".

Turkey had on August 24 began an unprecedented campaign inside Syria against IS and Kurdish militia which initially made rapid progress but has become mired in a deadly fight for the IS held town of Al-Bab since December.

The incident came with new CIA chief Mike Pompeo in Ankara for talks with Turkish officials on issues including Syria, on his first foreign visit since the inauguration of US President Donald Trump.

The fight for Al-Bab has been by far the bloodiest yet of Turkey's incursion inside Syria but the authorities have vowed to press on until its capture despite a mounting casualty toll.

Before Thursday's casualties were reported, the Dogan news agency said 66 Turkish soldiers have now been killed in the Syria operation since it began in August, mostly in attacks by IS.

- Revival in ties -

Turkey and Russia have been on sharply opposing sides in the Syria conflict, with Moscow supporting the regime of President Bashar al-Assad but Ankara pushing for his ouster as the key to peace.

Relations reached a dangerous low in November 2015 when Turkish warplanes shot down a Russian fighter jet over the Syrian border.

But a normalisation deal was reached over the summer and the two sides have been working ever more closely over the Syrian conflict.

They secured a deal to evacuate Syrians from Aleppo after the city was retaken by Assad backed by his Russian allies.

The two sides have since backed a process in the Kazakh capital Astana to search for peace to end the almost six-year civil war in Syria.

And Russian jets have on occasion carried out air strikes in Al-Bab in support of the operation.

Separate operations by Turkey and Assad's forces, backed by Moscow, has trapped the jihadists inside Al-Bab which has been besieged since Monday when Syrian forces cut off a road leading into the town.

There has been concerns of the risk of accidental contact in the busy skies above Syria although these have usually surrounded Turkey and Syrian regime forces.

Erdogan's spokesman Ibrahim Kalin said Wednesday Turkey had been coordinating with Russia to avoid any risk of contact with the Syrian regime forces.