(adds Merkel interview)

BRUSSELS, March 12 (Reuters) - NATO's secretary-general has said a proposed U.S. missile defence system risks splitting the alliance between those the programme would protect and those it would not, the Financial Times reported on Monday.

"When it comes to missile defence, there shouldn't be an A-League and a B-league within NATO," the newspaper quoted Jaap de Hoop Scheffer as saying in an interview. "For me it is the indivisibility of security that is the guiding principle."

Many NATO allies are concerned about the U.S. system which would be based in Poland and the Czech Republic to shoot down missiles fired by what Washington calls "rogue states" such as Iran and North Korea.

In Berlin, German Chancellor Angela Merkel was quoted as saying differences over the planned shield should be resolved within NATO and Russia should also be consulted.

Moscow regards the system as an encroachment on its former sphere of influence and an attempt to shift the post-Cold War balance of power. Senior politicians in Germany and France have warned the shield could stir up old enmities in Europe. "We, and I will say this in Poland, prefer a solution within NATO and also an open discussion with Russia about it," she said according to advance excerpts from an interview due to be broadcast on Tuesday on ZDF state television.

Merkel will begin a two-day visit to Poland on Friday. Last week Polish officials, including the deputy foreign minister, said Warsaw needed a bilateral security pact with the United States because it was concerned NATO lacked the resolve to counter any serious threats.

The Financial Times quoted NATO officials as saying the U.S. programme would protect almost all of Europe but not the southeast which would need an extra, shorter-range system because of its proximity to Iran.

The paper quoted de Hoop Scheffer as saying the U.S. programme could be complemented by existing NATO plans to put a battlefield missile defence system into operation by 2010.

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

De Hoop Scheffer made clear he believed there was a real missile threat to Europe.

"There is every reason to believe that, given the North Korean missile tests and the Iranian capability and what the Iranians are saying," the FT quoted him as saying.

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