The El Mundo newspaper had reported the Argentine forward was offered a five-year 250 million euro net (220.16 million pounds) deal, with City also prepared to pay a 250 million release clause.
It said City's chief executive Ferran Soriano, a former Barcelona general manager, and Messi's father and agent Jorge discussed a deal at the height of a political crisis in Catalonia over a campaign for independence from Spain.
Guardiola, a former Barcelona player and manager, said on Friday he had not tried to sign Messi at any of the clubs he had managed after leaving Spain.
News that makes sense
Your trusted source for staying up-to-date with the world around you. Get free daily news updates and analysis, straight to your inbox.
"When I left Barcelona and I went to Bayern Munich and Manchester City I never, never asked Lionel Messi to come to join Bayern Munich or here when I was manager," he told reporters.
"I never went to both clubs and said I want this player. Never.
"I know how important is this guy for Barcelona. Myself, I never spoke with the clubs, I never made the first step to say I want this player. Never.
"I said a thousand times I want him to stay at Barcelona."
Barca's all-time top scorer signed a new contract last November, seven months before his old deal expired. It runs until June 2021 and now contains a 700 million euro ($843 million) buy-out clause.
El Mundo reported in January that Messi had a clause in it allowing him to leave Barcelona without a transfer fee if Catalonia ceded from Spain and the club did not compete in any of Europe's top four leagues.
(Reporting by Alan Baldwin, editing by Toby Davis)
