Manafort has been voluntarily producing documents to congressional committees investigating Russia's interference in the 2016 presidential election. The search warrant indicates investigators may have argued to a federal judge they had reason to believe Manafort could not be trusted to turn over all records in response to a grand jury subpoena.
It could also have been intended to send a message to President Trump's former campaign chairman that he should not expect gentle treatment or legal courtesies from Mueller's team.
The documents included materials Manafort had already provided to Congress, said people familiar with the search.
"If the FBI wanted the documents, they could just ask [Manafort] and he would have turned them over," said one adviser close to the White House.
Josh Stueve, spokesman for Mueller, declined to comment, as did Reginald Brown, an attorney for Manafort.
"Mr Manafort has consistently cooperated with law enforcement and other serious inquiries and did so on this occasion as well," said Maloni, the spokesman for Manafort.
Mueller has increased legal pressure on Manafort, consolidating under his authority a series of unrelated investigations into various aspects of Manafort's professional and personal life.
Manafort's allies fear that Mueller hopes to build a case against Manafort unrelated to the 2016 campaign, in hopes that the former campaign operative would provide information against others in Trump's inner circle in exchange for lessening his own legal exposure.
The significance of the records seized from Manafort's apartment is unclear.
Manafort has provided documents to both the Senate Judiciary Committee and the Senate and House intelligence committees. The documents are said to include notes Manafort took while attending a meeting with Donald Trump Jr. and a Russian lawyer at Trump Tower in June 2016.
Emails show Trump Jr. took the meeting and invited Manafort after he was promised the lawyer would deliver damaging information about Hillary Clinton as part of a Russian government effort to assist his father's campaign.