Atlanta-based US District Judge J.P. Boulee rejected Fulton County's request for the return of original copies of the seized material.
Lawyers for the county had argued the FBI's search of its election hub relied on faulty and discredited evidence and violated protections under the US Constitution.
Boulee determined there were flaws in an FBI affidavit used to secure a judge's permission for the search, but concluded those shortcomings did not amount to "callous disregard" for the county's rights, the legal standard required to have the records returned.
"While the Affidavit was certainly far from perfect, this is not a situation where an officer left out all the facts that might undermine probable cause or where an officer intentionally lied," Boulee wrote in a 68-page ruling.
Spokespeople for Fulton County, the FBI and the Justice Department didn't immediately respond to a request for comment.
The ruling is a rare court victory for Trump's Justice Department in investigations that Trump has demanded. It will allow the FBI to keep possession of more than 600 boxes of 2020 ballots as it pursues a criminal investigation into whether election records were not properly retained or whether residents in Fulton County were defrauded out of a fair election.
But the investigation still faces significant obstacles. DOJ lawyers have not identified any individual targets of the probe and have not disputed claims that the statute of limitations appears to have expired on both crimes prosecutors have said they are investigating.
The dispute was closely watched by US election officials and experts across the country as Trump continues to threaten a potential federal government takeover of some local elections and sows doubts about voting ahead of the November elections.
Trump has continued to falsely claim that his defeat in the 2020 election to Democrat Joe Biden was the result of widespread fraud and has deployed US law enforcement and intelligence agencies to reinvestigate claims about the collection and tallying of votes.
Justice Department lawyers argued Fulton County had not met the stringent legal standard necessary to secure the return of material seized during a court-approved search.
During the search, which was approved by a federal magistrate judge, FBI agents seized original 2020 ballots and other records from the county's election centre in Union City, Georgia.
Authorities cited alleged "deficiencies or defects" with the 2020 vote, including claims that some digital images of ballots were missing and some absentee ballots did not appear to have been folded as required.
