The Football Association on Friday charged Guardiola, saying the symbol sported by the former Barcelona boss on his jacket broke its rules.
Guardiola was born in Catalonia and is revered in the region because of his links with Barcelona's soccer team, as both a player and coach.
The contract Messi signed last November includes a clause that he must remain at Barca only as long as the club is playing in a top-level European league.
On Thursday eight ministers of the deposed Catalan government, following the enforcement of home rule by the Spanish government, were detained pending a possible trial for their roles.
Spain on a knife's edge as Madrid takes direct control over Catalonia, fires defiant separatist leaders
Rajoy said he had also formally removed Catalonia's separatist leader Carles Puigdemont and his executive from office as part of measures to "restore normality".
On Sunday, the people of Catalonia voted in a referendum that was banned by the Spanish government. They voted 'yes' or 'no' to the question of independence from Spain.
Hundreds of people started gathering at polling stations in Catalonia to vote in an independence referendum banned by Madrid.