Pique has refused to back down over his support for Catalonia independence and the region's referendum.
Messi is fed up with Pique's behaviour, believing it can be detrimental to the team and their ambitions this season.
Okdiario pundit Eduardo Inda, speaking on El Chiringuito, revealed Messi had spoken to Pique this week about his concerns.
Inda stated: "Messi is afraid that the political path that has taken Barcelona could affect football fields with jeers for the team and the other day in the match with Atletico Madrid there was proof of it.
"That's why Messi took Piqué aside and told him: 'You must stop getting involved in political issues'.