"No-one can doubt my commitment to the Spanish national team", said the defender, who added it was "impossible" for everyone to share the same views.
Spain's Interior Ministry said that 431 members of the security forces were injured.
And Barca players - including their non-Spanish players such as Messi and Luis Suarez - will join the country in a national strike on Tuesday.
"Why would someone in favour of independence not want to play for Spain?". He endured chants, sometimes laced with expletives, of "Spain is your nation". Policed deemed one of the cards too offensive and removed it.
Thiago Alcantara says Spain teammate Gerard Pique is accustomed to dealing with "hostile treatment" by fans and does not believe the Barcelona defender will be affected if, as expected, he hears boos during Friday's World Cup qualifier against Albania in Alicante. He criticized police again on Monday on Twitter.
Pique said that he didn't see a problem with a separatist, which he said was not his case, to keep playing for the Spanish national team.
Spain play Albania in Alicante on Friday and will effectively qualify for Russian Federation 2018 with a victory given their superior goal difference over nearest rivals Italy. It beat Las Palmas 3-0.
Previously stating that he would not have an issue stepping down from La Furia Roja if his political stances were a problem, harsh taunting from fans during a Barcelona training session appears to have sparked a desire for Pique to continue fighting for his place in Julen Lopetegui's squad.
As police stormed makeshift polling stations on Sunday in Catalonia's unofficial referendum, Barcelona asked the Spanish league to postpone its scheduled game.
Motivation: "This is a game the whole world will be watching. It was an extraordinary measure for an extraordinary moment".
Asked if players should be able to talk about politics he said: "I understand the players that don't want to talk about politics because it's a drag sometimes". At one point it was coached by the late Dutch great Johan Cruyff. "In the end, what we did lasted for 90 minutes".
Catalonia's leaders have since claimed the autonomous region will declare independence from Spain in the coming days after officials claimed support of independence was 90% - albeit with a turnout of 42%.
"That's the million-dollar question", he said in reference to independence. The club played in an empty Camp Nou on Sunday to show its discontentment with the government's actions during the referendum.