The midfielder was not selected following his absence from two friendly matches against Russia and Italy last season.
CBF president Jose Maria Marin questioned Ramires' commitment to the national team, suggesting the 26-year-old was attending his wife's dinner party.
But a Chelsea spokesman said: "Contrary to media reports, Chelsea Football Club can confirm that Ramires was not available to play for Brazil in friendly matches against Russia and Italy in March of this year due to injury.
"The left adductor muscle injury was confirmed following an MRI scan and he underwent treatment at Chelsea FC's medical department from March 17 to March 28.
"Throughout this time information was relayed to the Brazilian national team doctor in the usual way and the treatment was agreed between the club and national team.
"However, Chelsea FC would like to apologise that it was not made clear when Ramires would be able to report back to the national squad."