Erdogan said he expected the support of NATO countries in Turkey's fight against "all terror groups" including the Kurdistan Workers Party (PKK), Islamic State (IS) jihadists and the group blamed by Ankara for the failed July 15 coup.
He called on the European Union to tighten its approach to the PKK, which Brussels designates as a terror group but whose members, according to Erdogan, are allowed to roam freely within the bloc.
Turkey has been a member of NATO since 1952 but its bid to join the European Union has been further set back by disputes over the magnitude of its crackdown in the wake of the coup.
Erdogan had at the weekend mooted that Turkey could join the Shanghai Cooperation Organisation (SCO), a loose security and economic bloc led by Russia and China sometimes seen as an eastern counterpart to NATO.
But he did not refer to this in his speech in Istanbul to the NATO meeting.
Pressed by a Dutch lawmaker to condemn the crackdown that has seen over 35,000 arrested, Stoltenberg said he had told Turkish leaders all measures had to be taken within the rule of law.
He said he welcomed cooperation between Turkey and the Council of Europe over the legal measures after the coup, saying this should be an "important tool" to ensure the rule of law and human rights are applied.
Stoltenberg also made no reference to Turkish officers serving in NATO command posts who he had said last week had asked for asylum following the failed coup.
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