Jaap de Hoop Scheffer, Nato secretary general, discussed missile defence with the Financial Times and its sister paper FT Deutschland, in a conversation that made clear his conviction that Europe should establish its own system to complement Washington’s.

Although Mr de Hoop Scheffer did not want to enter into specifics about how many European countries would be covered by the US’s own missile defence programme, he argued that the threat to the continent was indisputable and could be countered by a European-wide system.

The FT has separately discussed with Nato officials how such a system would focus on southeastern European countries whose security could not be assured by the US programme – principally Turkey, Italy and Greece – and how it could build on the developments made by the US system.

One possibility hinted at by Mr de Hoop Scheffer would be to use Nato’s own “theatre missile defence” programme to plug the gap left by the US programme. Under this scenario, south-eastern Europe would be protected by Patriot missiles and Aegis radar connected to the smaller scale Nato system.

This is an edited transcript of the interview.

DE HOOP SCHEFFER: If you ask me how Nato could play a role or how Nato allies could play a role in missile defence, we have homework to do. I have homework to do.

The heads of state and government [at a Nato summit in Riga last year] have asked us and me - I’m supposed to lead that process - to discuss the threat from a military perspective, from a political perspective. Our defence ministers meeting here in June can continue the discussion.

At the same time we see the US entering into bilateral discussion with the Czechs and the Poles. The Danes have their radar system, the UK has its radar system, so I think in total there are five nations involved. But the important thing is now the US and Poland and the US and the Czech Republic. It’s not my job to enter into that discussion, although the result is relevant for Nato. For me it is indivisibility of security that is the guiding principle.

We are already moving forward with developing systems to protect deployed forces, rather than population centres and territories. There could be at a later stage a relationship between the two systems.

FT: When the Germans ask for these bilateral deals between the US and Poland and the Czech Republic to be dealt with here in Nato and the Nato Russia council how much scope do you see for this?

DE HOOP SCHEFFER: When I listen to [defence minister Franz Josef] Jung and Chancellor [Angela] Merkel they are not saying ‘Nato should discuss the bilateral issues between the US and Poland and the US and the Czech Republic’ .

Nato as such should not take the position of in any way influencing the negotiations of the US and the Czech Republic and the US and Poland. I see that as a bilateral trajectory which is made transparent because of the US briefings to the Nato Russia Council and to the North Atlantic Council [of Nato ambassadors].

Missile defence in general is a subject which is a very Nato relevant subject. How we are going to do it in the end is still too early to tell. We have a feasibility study that says it is theoretically very possible to use missile defence to protect Europe as a whole. But it needs political discussion. It needs a discussion on who is going to pay what.

FT: Do you think there is anything else to explain to the Russians or has everything been said already?

DE HOOP SCHEFFER: Well quite honestly that is for me very difficult to answer because I do not know what exactly has happened in these last meetings the Americans have had with the Russians. I accept the American reasoning that they have talked to the Russians extensively and that they have given them all kinds of information.

I cannot speak for the American-Polish-Czech trajectory. That is not my job. And it’s not my job to slow those negotiations down. I’ll not do that. Because I think the threat is real. And I think it is a good decision that the Americans took. From a Nato perspective, I think we should be transparent with the Russians.

What would not be helpful would be for Russian generals to go on and on and say that this is against them. That is not a good basis for discussion because they should be convinced that it is not. And even I as a layman can explain to them that it is not. You don’t need to be a technological wizard or an Einstein to understand that this cannot be possibly directed against the Russians and cannot diminish their first strike capability.

FT: Do you think this is because the Russians are afraid of a further militarisation of space?

DE HOOP SCHEFFER: If there is a Russian perception, it is of being encircled. I underline that I think the perception is wrong. Because I do not understand how anybody can be worried about democracy and stability and the rule of law coming closer to their borders. This is a phrase I borrow from the president of Estonia who was the first one to use it. But if there is a perception in Moscow that they are encircled we have to take that perception seriously. And I’ll take that perception seriously although I think it is wrong.

FT: Can you convey how crucial you consider the missile threat to be?

DE HOOP SCHEFFER: If the allies and I had not been convinced about the fact that there is a threat I think a) the decision to do the feasibility study would not have been taken and b) we would not have seen the Riga tasking.

I do not exclude that in the subsequent discussions there will be nuances in the positions of the allies about the threat. I don’t exclude that. But from what I have noticed formally around the Nato table and informally I do not think that you will see in Nato a very fundamental or basic discussion about a threat.

FT: Is there a basic acceptance of the threat?

DE HOOP SCHEFFER: I think there is. And I think there is every reason to believe that, given the North Korean missile tests and the Iranian capability and what the Iranians are saying and the political stance they’re taking. Do not forget that, when we discuss missile defence, it is a defensive debate. It is not a debate about wanting to be offensive in any way. It is only defensive. It will only work against incoming missiles. And nothing else. That’s the limit.

There will certainly be a discussion about threat perception. Twenty six democracies sitting around the table will by definition have a discussion, have a debate. I should be the last to worry if under my leadership there should be a debate in the Nato council.

FT: What would it do to the solidarity of the alliance if some parts were not covered by the system?

DE HOOP SCHEFFER: For me the indivisibility of security is key. When it comes to missile defence, there shouldn’t be an A-league and a B-league within Nato. But I do not think it will not come to that. Because I think we will in the end agree about threat perception.

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