A US State Department spokeswoman confirmed the search had taken place but would not make further comment.
"All inquiries regarding the search of the United States' residence of Nigerian Vice President Atiku Abubakar should be directed to the Department of Justice," she said.
The Justice Department declined to comment.
The raid, which took place on 3 August but has just come to light, was in connection with an investigation into William Jefferson, a Democratic legislator from New Orleans, the city's Times-Picayune newspaper said on Saturday.
The Nigerian vice president was not available for comment on Sunday, but a Nigerian presidential spokeswoman said: "The presidency has been notified of the incident and is using diplomatic channels to find out the reason and the findings surrounding the incident."
A source familiar with the investigation said subpoenas showed federal agents were looking for records indicating whether Jefferson paid, offered to pay or authorised payments to Nigerian or Ghanaian government officials, The Times-Picayune said.
Agents were seeking documents related to Jefferson's dealings with Abubakar and the vice president of Ghana, Aliu Mahama. Jefferson returned from a five-day visit to Ghana in mid-July, about three weeks before the FBI raided his homes, according to the newspaper.
Vice President Atiku Abubakar was
sworn in for a second term in 2003
The subpoenas focused partly on a telecommunications deal Jefferson was trying to engineer in Nigeria over the past year, according to documents and those familiar with details of the investigation.
According to The Times-Picayune, sources familiar with the telecommunications deal said Jefferson was attempting to smooth the way for iGate Corp., a small Kentucky company, to offer its high-speed broadband technology to Nigeria's fast-growing telecommunications market.
Jefferson's spokeswoman, Melanie Roussell, said the eight-term legislator would continue to decline comment on the federal investigation. He has only said he is cooperating with federal investigators, according to the newspaper.
Jefferson's attorney, Mike Fawer, has said he thinks the FBI had been conducting a sting operation against his client.
Abubakar and his wife, Jennifer, a doctoral student at American University in Washington, were said to be in Nigeria.