Trump, on his first visit to Brussels, also said Germany was selling too many cars, had a visibly awkward handshake with the new French president, and pushed aside the Montenegrin leader at a joint photo.
And Stoltenberg said later that Trump, Vice President Mike Pence and other US officials have stated clearly their assurances.
The act was being widely denounced online.
"It didn't really register", he told reporters after the summit.
The rebuke was being criticized by opponents. He was trying to reach the front of the group to take the position reserved for him next to NATO Secretary General Jens Stoltenberg and the British Prime Minister Theresa May.
"That is not fair to the taxpayers of the United States", he said.
Reaction to the summit and Trump's visit was swift, with Charles Michel, the Prime Minister of Belgium whose country has hosted North Atlantic Treaty Organisation for over 50 years, warning, "Security today requires much more than the traditional military tools".
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Reuters was not able to confirm their authenticity. "The situation is terrifying", she told Reuters by phone. It accuses elements of the opposition of seeking to overthrow it by force with help from arch-foe Iran.
But first Trump has one more day in Sicily, which will include discussions of global economy and climate, a meeting with small African nations - Trump will be seated between the leaders of Niger and Tunisia - and migration issues.
German Chancellor Angela Merkel struck an entirely different note as she unveiled a memorial made up of a section of the Berlin Wall to mark the end of the Cold War.
Milan Knezevic, leader of Montenegro's opposition and anti-Nato Democratic People's Party, said by phone that Trump's behavior "is clear proof that there's no such thing as equality in Nato", showing that the country is just a "smudge" on the alliance's map.
"This is not fair to the people and taxpayers of the United States, and many of these nations owe massive amounts of money from past years and not paying in those past years", declared the USA commander-in-chief. "And we must be vigilant", Mr Trump told the summit.
President Donald Trump speaks at NATO Headquarters in Brussels, May 25, 2017. Sicily is on the front lines in Europe's migration crisis, the first landfall for most of the more than 180,000 migrants who arrived in Italy past year and the reason the Italian government chose Sicily as the backdrop for this summit. French President Emmanuel Macron, Italian Premier Paolo Gentiloni, who is serving as host, and British Prime Minister Theresa May are also making their debut, and the meeting is the first since the United Kingdom voted to exit the European Union, which is also represented at the gathering.
After the next 24 hours of meetings, the president returns to Washington on Saturday.
James Comey, the former FBI director who led the Russian probe until Trump abruptly fired him, is still expected to testify before Congress about memos he kept on conversations with the president that involved the investigation.