Brazil boss Fernando Diniz has made the decision to remove Paqueta from his squad ahead of the Selecao’s upcoming international fixtures.
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Interim head coach Diniz had originally called the 25-year-old up to the squad, but has since reversed his decision as he looks to “protect” him.
Speaking to Globo Esporte about the change of heart, he said: “I’m a guy who… what protects me my whole life is the truth. Paqueta was on the list.
“He’s a player I like a lot. It’s a question of preservation, letting him resolve these issues, which go beyond the game.
“Make him more comfortable to resolve. We had these problems here in Brazil, this needs the time factor for things to clear up. He’s a player I adore, even though we’ve never worked together.
“The CBF will have its doors open to receive him as soon as he positively resolves these issues we had at the last minute.”
Paqueta was on the brink of a move to treble winners Manchester City, but has seen the deal break down.
The Cityzens had submitted a £70million offer, however they are now said to be waiting to see the result of the probe.
The FA’s investigation is believed to be surrounding wagers placed in Paqueta’s home country of Brazil.
The attacking midfielder joined The Hammers last summer in a club record £51.4million deal from French outfit Lyon.
He made 28 Premier League appearances for the East London club last season, netting four times and registering a further three assists.
There has been other recent betting probes into Premier League footballers that have resulted in lengthy bans.
Brentford striker Ivan Toney is currently serving an eight-month ban for breaching 232 of the FA’s betting rules.