NATO allies will strive to convince Moscow this week that their European missile shield is not aimed at Russia after the Kremlin threatened to deploy weapons systems near EU borders.

US Secretary of State Hillary Clinton will join her 27 NATO counterparts for talks on Wednesday that will also touch on the security transition in Afghanistan, ties with the Arab world and tensions in Kosovo.

They will then meet with Russian Foreign Minister Sergei Lavrov on Thursday to tell him the missile shield will go ahead but that NATO still wants to negotiate a cooperation deal with Moscow, alliance diplomats said.

"Rather than having threats to NATO in response to the deployment of NATO missile defences, it would be better if NATO and Russia were to cooperate on dealing with the threats that we face in common," said a senior NATO official.

A diplomat said NATO wants to "calm things down" after Russia activated a radar warning system against incoming missiles in its exclave of Kaliningrad on the EU's borders last week.

Days earlier President Dmitry Medvedev threatened to deploy missiles in Kaliningrad but he left the door open for continued dialogue on NATO's defence system one year after he agreed to explore ways to cooperate.

"We have been clear and I assume we will be clear in the ministerial that NATO missile defenses will go ahead, ... that those defences are not directed against Russia," the senior NATO official said.

Western officials insist that the missile shield is targeted against growing threats from the Middle East, especially Iran.

NATO has sought to improve ties with Russia in recent years, and Moscow has allowed the alliance to use its territory to send vital supplies to troops in Afghanistan.

The transit route through Russia has become all the more important since Pakistan shut down supply lines in anger at a NATO air strike on the Afghan border which killed 24 Pakistani troops last month.

The uneasy relations with Pakistan will not be on the agenda.

But ministers will discuss the transfer of security reins to Afghan forces following Monday's major Afghanistan conference in Bonn, where participants vowed sustained support for another decade after combat troops leave in 2014.

A peacekeeping mission closer to home, Kosovo, will be discussed in the wake of violence at the border with Serbia that injured 50 NATO troops.

The alliance wants Serbs living in northern Kosovo to remove barricades that have stoked tensions with the ethnic Albanian authorities in Pristina, three years after Kosovans declared independence.

And after the end to the NATO air war in Libya on October 31, in which Qatar, the United Arab Emirates and Jordan played key roles, the alliance wants to see how the Arab Spring "may provide new opportunities for engagement with countries from the Middle East and north Africa," the senior official said.