NATO "is now directing the standing maritime group to move into the Aegean without delay and start maritime surveillance activities", Stoltenberg told a press conference after alliance defence ministers backed the move.
He said the migrant crisis, driven by conflict and turmoil across the Middle East and North Africa, was the worst since World War II and posed a major security threat to the 28-nation alliance.
NATO Standing Maritime Group 2, currently under German command, comprises three ships and allies had promised more so it can carry out "reconnaissance, monitoring and surveillance in the Aegean Sea," he said.
NATO would work closely with the European Union and its border control agency Frontex, he added.
German Chancellor Angela Merkel joined forces with Turkey on Monday to request help from the 28-nation alliance as thousands more refugees fled heavy fighting around the Syrian city of Aleppo.
Turkey -- the only Muslim-majority nation in NATO and with one of its largest armies -- was the main transit country for the more than one million migrants who reached Europe last year.
