The newspaper also said the FBI has asked Clinton lawyer David Kendall about the security of a thumb drive, containing copies of Clinton's emails, that Kendall possesses.
The Post report cited two anonymous government officials, but said Kendall confirmed that the government was investigating the security of the devices.
Clinton's emails have been under scrutiny since it was revealed she used a private server in her Chappaqua, New York, home while she was the top US diplomat.
Last month, the inspector general of the US intelligence community alerted the Justice Department about classified information included improperly on email that went through Clinton's home server. The referral to the Justice Department did not seek a criminal probe and did not specifically target Clinton.
The two officials cited by the Post also said that the FBI was not targeting her.
A spokesman for Clinton's presidential campaign tweeted yesterday that that Post story "doesn't change anything ... IG sent ask to DOJ to confirm emails are secure."
An FBI spokesman contacted last night by The Associated Press declined to comment, and Kendall did not respond immediately to an emailed request for comment.
State Department spokesman Mark Toner was asked last week whether the department would be "open" to having the FBI examine the thumb drive. "We've made sure that the documents at her lawyers' are in a secure setting, but I'm not going to speak to what the FBI should or shouldn't do," Toner responded.
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