Mr Johnson added ahead of a meeting in Brussels that this was "a key moment to discuss Russian Federation with foreign ministers of all 29 allies".
Even before his confirmation on Thursday, the former Central Intelligence Agency director was already involved in USA diplomacy, although this is first meeting at Nato, an organisation founded on defence against the threat from the former Soviet Union.
In February, an unnamed USA official told the Turkish newspaper Haberturk that this could "negatively influence the interoperability of NATO" and that the White House may introduce punitive measures in response.
Pompeo's presence at Nato was seen as crucial as the alliance prepares for a July 11-12 summit in Brussels where Nato leaders are set to agree a new deterrent to Moscow, including a command to defend the Atlantic in the case of conflict.
"We are in a situation where we've not been before", Stoltenberg said after the meeting.
They discussed ways to combat growing regional threats from both Russian Federation and Iran, and ways to strengthen the worldwide alliance.
According to a statement by Turkey's Foreign Ministry, Cavusoglu will "exchange views on the current security environment and review preparations for the upcoming North Atlantic Treaty Organisation summit to be held in Brussels" on July 11 and 12.
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He said: "When tensions are high, it is even more important to talk with Russian Federation".
Pompeo pressed allies to increase their military budgets to meet a target of 2% of economic output spent on defence every year by 2024, as well as ensuring 20% of the outlay is on equipment, a United States official said.
Nine have produced realistic plans for reaching it by 2024, but the rest, including Germany, have not.
Trump sent Pompeo to North Korea three weeks ago to meet the isolated country's leader, Kim Jong Un, ahead of a summit with the US president to address Pyongyang's nuclear programme.
Alliance members have undertaken the biggest reinforcement of collective defense since the end of the Cold War, Stoltenberg said.
Read alsoHead of NATO Military Committee General Petr Pavel: We are heading to make Ukrainian defense forces capable and credible enough to deter any potential aggressionHe said he was careful to describe consensus "when there were lots of different voices about how to approach it and what the right actions there ought to be to achieve it". A spokeswoman from State Department said that Pompeo will then go to Saudi Arabia, Israel and Jordan.