Messi, who captained Argentina at the World Cup, is yet to comment on when he may be available again, having skipped a pair of friendlies in September.
And Scaloni, in charge on a temporary basis as Argentina seek a successor to Jorge Sampaoli, is unclear on when he may be able to select Messi.
"I spoke with Messi about 10 days ago, after the talk we made the final decision he is not to be called up," Scaloni said at a news conference on Monday.
"We do not talk about what could happen in a while, we talked about how the team played because honestly Leo sees everything.
"But not beyond that because in my head we have not planned more than six games."
Messi has previously taken time away from Argentina following the 2016 Copa America Centenario after La Albiceleste lost to Chile on penalties.
However, the star would return and prove instrumental in Argentina qualifying for the 2018 World Cup, which the nation did on the final day of qualifying thanks to a Messi hat-trick against Ecuador.
While some no doubt hope Messi will again make his return to the team after a break, Argentina legend Diego Maradona has told Messi to retire from international duty, claiming he receives too much criticism for the team's results.
"The under-15s lose and it's Messi's fault," Maradona told Clarin. "The fixture in Argentina puts Racing against Boca and Messi is to blame. It's always his fault. I would say, 'Don't go anymore'. Let's see if they can handle it."
Meanwhile, Juan Foyth and Rodrigo De Paul have been called up to the Argentina squad for the first time for the upcoming Iraq and Brazil matches.