NATO allies meet Wednesday hoping to calm Russian fears over their missile shield project but US Secretary of State Hillary Clinton angered Moscow by criticising its parliamentary elections.

Clinton is joining her 27 alliance counterparts in Brussels for two days of talks that will also touch on the Afghan war amid tensions with Pakistan after a NATO air strike on the Afghan border last month killed 24 Pakistani troops.

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.

A diplomat said NATO wants to "calm things down" after Russia activated a radar warning system in its exclave of Kaliningrad on the EU's borders last week, days after President Dmitry Medvedev threatened to deploy missiles there.

"Some of President Medvedev's recent comments about NATO's missile defence system reflect a fundamental misunderstanding of the system," NATO Secretary General Anders Fogh Rasmussen wrote in Russia's Kommersant newspaper Tuesday.

The Russian threats "reflect the rhetoric of the past," Rasmussen said.

While he was pleased that Medvedev did not shut the door on dialogue, Rasmussen indicated that NATO will continue to refuse to provide legal guarantees that the system does not threaten Russia.

Western officials insist that the missile shield is aimed at countering Iran.

NATO and the United States have sought to improve ties with Russia since President Barack Obama took office in 2009.

But Clinton irked Russia by voicing "serious concerns" about the parliamentary elections and calling for allegations of fraud and vote-rigging to be investigated.

"As we have seen in many places, and most recently in the Duma elections in Russia, elections that are neither free nor fair have the same effect," Clinton said in Lithuania on Tuesday.

The Russian foreign ministry described Clinton's comments as "unacceptable" while Medvedev said it was "none of their business" what Russia's political system looked like.

Russian riot police arrested hundreds of activists in central Moscow on Tuesday to stop a new protest alleging that elections were rigged in favour of Prime Minister Vladimir Putin's ruling party.

Despite lingering suspicions between the former Cold War foes, Russia 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 last month's deadly air strike on the Afghan border. NATO has launched an investigation into the raid.

"We have every interest to make sure that we get back to a better relationship again and that is what we are trying to achieve in the near future," said a senior NATO official.

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

Another mission, Kosovo, will also be discussed in the wake of violence at the border with Serbia that injured 50 NATO troops.