Anders Fogh Rasmussen said NATO member Turkey could buy equipment from any source after Ankara raised the possibility of accepting a Chinese bid to build its first long-range anti-missile system.
"Our position is very clear. It's a national decision to decide which equipment to purchase," Rasmussen told a press conference at the close of the first day of a two-day NATO defence ministers meeting.
"However, seen from a NATO perspective, it's of utmost importance that the systems nations plan to acquire can work and operate together with similar systems in other Allied nations," he said.
Turkey's Defence Minister Ismet Yilmaz told the Vatan newspaper earlier this month China had provided the best price.
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A Chinese company beat competition from a US partnership of Raytheon and Lockheed Martin, Russia's Rosoboronexport, and the Italian-French consortium Eurosamrs for a deal worth some USD 4.0 billion.
NATO member Turkey is a key regional ally to the United States and currently has US-built Patriot missile systems deployed on its border to deter incoming attacks from Syria.
Rasmussen said ministers from the 28 member states had discussed missile defence against attacks from outside the Euro-Atlantic area, a reference in the past taken to mean Iran although the secretary general named no country.
Russia has voiced strong opposition to the missile defence plans, fearing they could jeopardise its own security.
Its Defence Minister Sergei Shoigu is likely to raise the issue tomorrow when he meets his NATO counterparts in the NATO-Russia Council.
Rasmussen said ministers also discussed increased cooperation, a necessary step to offset the impact of ever tighter military budgets, and increased large-scale exercises.