"Brazil practicing and Neymar participating normally in the team's activity", the federation said in a Twitter post.
He had been playing keep-away with a few other players when he started showing signs of discomfort in his ankle.
"He was feeling pain thanks to the large number of fouls he suffered in the Switzerland game", a spokesman told reporters. "Since today was only a recovery session for the starters, and he complained about pain, he ended going to rehabilitation".
Four years ago, defeating Uruguay and Brazil in their group, reaching the quarterfinals, and along with a draw from England, Costa Rica's team will open their campaign against Serbia in the FIFA World Cup 2018 today on Sunday.
Neymar had already practiced separately from his teammates on Monday.
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I suppose we will only know the answer to that question when the next couple of matches are played in that Group and I do think all eyes will be on Switzerland to see just how they get on in those matches for sure!
Brazil media officer Vinicius Rodrigues stressed the issue was not associated with Neymar's foot, which required surgery in February, as he highlighted the fact the 26-year-old was fouled 10 times in Rostov-on-Don - the highest total since the 1998 World Cup.
The Paris St Germain forward was subdued in the match and unrecognisable from the man who became the world's most expensive footballer when he left Barcelona last August to join the French champions. But fans were shocked when Brazilian playmaker sported an unruly mop of blonde hair for his nation's World Cup opener against Switzerland.