She said that after the initial audit report the NBPA report had been frozen "due to inadequate financial controls and a lack of other financial management procedures".
Auditors are now completing a review of the NBPA's accounts in an ongoing investigation.
The spokesperson added that any evidence of improper activities would be presented to the department's fraud team.
It "may involve separate investigation or [investigation from] home [police] boards", she added.
The NBPA was launched in 1994 in an effort to prevent the rapid loss of black staff from the Metropolitan police.
It states on its website that its primary mission is "to improve the working environment of black staff by protecting the rights of those employed within the police service and to enhance racial harmony and the quality of service to the black community of the UK".
Commenting on the news, the chair of the Independent Police Complaints Commission (IPCC), Nick Hardwick, said that the commission has been aware of the concern over NBPA funds since January.
"At that time it was apparent that the Home Office had been commissioned to carry out an audit of the National Black Police Association and we were satisfied that this was an appropriate response," he said.
"We are maintaining contact with the audit team and should they identify any prima facie evidence of criminality or misconduct we will then consider our response and take the necessary action."
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