One of the flares was thrown from the section containing travelling spectators into another housing home fans below during Saturday's 3-1 Premier League victory for the champions on Tyneside.
A Northumbria Police statement said: "A flare was thrown from the section containing Manchester City fans into a section of Newcastle United fans, no one was injured and it was quickly extinguished. A second flare was set off in the section containing Manchester City fans."
The statement went on: "Officers at the scene carried out extensive enquiries, including checking CCTV and speaking with available witnesses. However, the person or people responsible are yet to be identified.
"We take incidents such as this extremely seriously and enquiries are still ongoing. Officers continue to work with colleagues at Greater Manchester Police."
The investigation is one of two launched by the Northumbria force following the game.
They also received a complaint involving an allegation of racist abuse after City substitute Aleksandar Kolarov become involved in a lengthy exchange with fans holding an Albania flag as he warmed up on the sidelines.