Speaking to journalists during a court appearance in Moscow, Paul Whelan said: "I was injured in the prison... the prison doesn't want to tell you."
He added: "I am standing here in great pain due to an injury sustained in the prison by the prison guards."
Mr Whelan, who holds four passports - including a British one - is being held on accusations that he had received Russian state secrets.
He insists that he was framed, and that the USB drive he took from an acquaintance was meant to contain holiday photos, not state secrets. The Whelan family also claims that he was in Moscow for a friend's wedding.
During his court visit, Mr Whelan requested hospital treatment. After he was evaluated by medics, the judge deemed that hospital care was not necessary.
Mr Whelan did not specify the nature of his injury but his lawyer later claimed that guards had made him carry heavy items to another cell in the prison, exacerbating a pre-existing hernia.
His lawyer, Vladimir Zherebenkov, also claimed that his client formally requested an operation for his aggravated hernia, and that the request will be properly filed soon.
Mr Whelan also claimed that he was only given two hours to prepare a defence and that no documents supplied for his hearing had been translated into English.
The US embassy in Moscow is attempting to establish contact with Mr Whelan concerning his “serious health allegations”, and has requested “immediate consular access” on Twitter, AFP reports.
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Mr Whelan had previously pleaded to Donald Trump for his freedom, saying: "Mr President -- we cannot keep America great unless we aggressively protect and defend citizens wherever they are in the world.”
His arrest was extended to October 29, 2019.