A new European Union defence pact and Turkey's offensive against US-backed Kurdish fighters in Syria have put strains on a transatlantic alliance facing a more assertive Russia and threats from the Middle East.

NATO defence ministers met late Wednesday with EU foreign policy chief Federica Mogherini to discuss their concerns over duplication after Brussels agreed in December to a new defence pact.

"There is a clear understanding to include in written EU documents that the common defence is a NATO mission and a NATO mission alone," Mattis told a press conference in Brussels.

Mattis said discussions were "very candid" between the 29-nation NATO, which includes European Union members, and Mogherini.

"We have sufficient rigour in the political sharing, the political discussions, to keep the EU effort, for example on military mobility," Mattis said.

He said the EU can "enhance NATO common defense capabilities and does not draw from them."

The EU's so-called permanent structured cooperation on defence agreement, known as PESCO, has projects in view already to develop new military equipment and improve cooperation and decision-making.

But on Sunday a senior official working with Mattis said Washington had concerns that some of the proposed initiatives risked "pulling resources or capabilities away from NATO".

- 'Common ground' -

In the runup to the meeting, NATO secretary general Jens Stoltenberg warned there was "no way" the EU could replace the transatlantic alliance in guaranteeing European security.

"It will be absolutely without any meaning if NATO and the EU start to compete," the former Norwegian premier told reporters on Tuesday.

A row that is potentially more serious is the one festering between the United States and Turkey over Ankara's "Operation Olive Branch", launched last month against the Syrian Kurdish People's Protection Units (YPG).

While Turkey views the YPG as a "terrorist" group, the United States has been working closely with the militia against the Islamic State group in Syria and giving it weapons, infuriating Ankara.

"We maintain an absolutely honest and open dialogue," Mattis said after meeting his Turkish counterpart Nurettin Canikli on the sidelines of the NATO meeting a day earlier.

"I think we are finding common ground," Mattis told the press conference on Thursday.

During the handshake for the talks on Wednesday, Mattis appeared stony-faced.

He called "for a renewed focus on the campaign to defeat ISIS, and to preventing any vestige of the terrorist organisation from reconstituting in Syria," the Pentagon said in a statement Thursday, referring to the Islamic State group.

- Legitimate threats to Turkey -

But he "acknowledged the legitimate threats posed to Turkey's national security by terrorist organisations," the statement said.

Mattis said NATO allies had made progress toward a goal they set in 2014 of raising defence spending to two percent of GDP over a decade but added much still needs to be done.

Since he took office more than a year ago, US President Donald Trump has warned NATO allies to meet the goal and NATO officials said they will be under close watch in the runup to an alliance summit in June.

Mattis and Stoltenberg said eight NATO members are set to meet the two percent target this year, adding a total 15 are expected to do so by 2024 while others fall short.

The ministers agreed here Wednesday to modernise the NATO command structure with plans to set up an Atlantic command to protect maritime routes between Europe and North America.

They also decided to establish a new support command to improve the movement of troops in Europe and boost troop rapid response while creating a new operations centre to defend against cyber attacks in Mons, Belgium.

Trump's administration has also asked the other 28 NATO member states, mainly European but also Canada, to increase their military capabilities and contribute more to war games.

The ministers agreed Thursday to start planning for a sustained NATO mission to train Iraqi forces, including setting up officer academies, as part of efforts to keep extremist groups at bay.