A spokesman for Mr. Mueller declined to comment. Lawyers and a spokesman for Mr. Manafort also declined to comment.
Few people can upend Washington like a federal prosecutor rooting around a presidential administration, and Mr. Mueller, a former F.B.I. director, is known to dislike meandering investigations that languish for years. At the same time, he appears to be taking a broad view of his mandate: examining not just the Russian disruption campaign and whether any of Mr. Trump’s associates assisted in the effort, but also any financial entanglements with Russians going back several years. He is also investigating whether Mr. Trump tried to obstruct justice when he fired James B. Comey, the F.B.I. director.
Mr. Manafort is under investigation for possible violations of tax laws, money-laundering prohibitions and requirements to disclose foreign lobbying. Michael T. Flynn, the former national security adviser, is being scrutinized for foreign lobbying work as well as for conversations he had last year with Russia’s ambassador to the United States. On Monday, Mr. Flynn’s siblings announced the creation of a legal-defense fund to help cover their brother’s “enormous” legal fees.
The wide-ranging nature of Mr. Mueller’s investigation could put him on a collision course with Mr. Trump, who has said publicly that Mr. Mueller should keep his investigation narrowly focused on last year’s presidential campaign. In an interview with The New York Times, Mr. Trump said Mr. Mueller would be overstepping his boundaries if he investigated his family’s finances unrelated to Russia.
For the moment, Mr. Mueller’s team has shown a measure of deference to White House officials, sparing them grand jury subpoenas and allowing them to be appear for voluntary interviews. Those sessions are expected to begin soon. Ty Cobb, a lawyer brought in to manage the White House response to the inquiry, has told administration officials that he wants to avoid any subpoenas from the special prosecutor.
Staff members have been working long hours answering Mr. Mueller’s request for 13 categories of documents, including records related to Mr. Comey’s firing and Mr. Trump’s role in drafting a misleading statement about a June 2016 meeting between campaign officials and Russian-born visitors. Nonetheless, the demand for documents has provoked at least one angry confrontation between Mr. Cobb and Donald F. McGahn II, the White House counsel, over whether certain documents should be withheld to protect the president’s right to confidentiality.
But associates of both Mr. Manafort and Mr. Flynn have received more peremptory treatment. Instead of invitations to the prosecutor’s office, they have been presented with grand jury subpoenas, forcing them to either testify or take the Fifth Amendment and raise suspicions that they had something to hide. At least three witnesses have recently been subpoenaed to testify about Mr. Manafort: Jason Maloni, a spokesman who appeared before the grand jury for more than two hours on Friday, and the heads of two consulting firms — Mercury Public Affairs and the Podesta Group — who worked with Mr. Manafort on behalf of Viktor F. Yanukovych, the pro-Russia former president of Ukraine.
Mr. Mueller’s team also took the unusual step of issuing a subpoena to Melissa Laurenza, a specialist in lobbying law who formerly represented Mr. Manafort, according to people familiar with the subpoena. Conversations between lawyers and their clients are normally considered bound by attorney-client privilege, but there are exceptions when lawyers prepare public documents that are filed on behalf of their client.
Mr. Mueller took over the Russia investigation in May, after the F.B.I. had already spent nearly a year looking into connections between Mr. Trump’s associates and Russians. His team has occasionally been caught by surprise, hearing of possibly important information only when it is revealed in the news media.
This was the case in July, when Mr. Mueller’s prosecutors learned about email exchanges between Donald Trump Jr. and an emissary for a Kremlin-connected Russian oligarch only after they were disclosed in The New York Times, according to a law enforcement official who spoke on condition of anonymity. Donald Trump Jr., the president’s son, set up the Trump Tower meeting to receive what he was told would be damaging information about Hillary Clinton from the Russian government.
Soon after his name surfaced, one of the Russian-born participants at the meeting, Rinat Akhmetshin, was ordered to testify before the grand jury, according to one of Mr. Akhmetshin’s associates.
“They seem to be pursuing this more aggressively, taking a much harder line, than you’d expect to see in a typical white collar case,” said Jimmy Gurulé, a Notre Dame law professor and former federal prosecutor. “This is more consistent with how you’d go after an organized crime syndicate.”
The tactics reflect some of the hard-charging — and polarizing — personalities of Mr. Mueller’s team, seasoned prosecutors with experience investigating financial fraud, money laundering and organized crime.
Admirers of Andrew Weissmann, one of the team’s senior prosecutors, describe him as relentless and uncompromising, while his detractors say his scorched earth tactics have backfired in some previous cases. Greg B. Andres, another one of Mr. Mueller’s prosecutors, once ran an investigation into a Mafia kingpin. Zainab N. Ahmad made her name as a prosecutor pursing high-profile terrorism cases.
Some lawyers defending people who have been caught up in Mr. Mueller’s investigation privately complain that the special counsel’s team is unwilling to engage in the usual back-and-forth that precedes — or substitutes for — grand jury testimony. They argue that the team’s more aggressive tactics might end up being counterproductive, especially if some grand jury witnesses turn out to be more guarded than they would have been in a more informal setting or invoke the Fifth Amendment.
The longer Mr. Mueller’s investigation goes on, the more vulnerable he will be to allegations that he is on a fishing expedition, said Katy Harriger, a professor of politics at Wake Forest University and the author of a book on special prosecutors. Such accusations dogged the investigation of Kenneth W. Starr, the independent counsel whose investigation of Mr. Clinton stretched on for years.
To a degree, Mr. Mueller is in a race against three congressional committees that are interviewing some of same people who are of interest to the special prosecutor’s team. Even if the committees refuse to grant them immunity, congressional testimony that becomes public can give other witnesses a chance to line up their stories.
Rep. Adam Schiff of California, the top Democrat on the House Intelligence Committee, said committee staff members were going to great lengths not to get in Mr. Mueller’s way. But Senator Charles E. Grassley, the chairman of the Senate Judiciary Committee, indicated last week that his committee might subpoena witnesses to testify about the circumstances of Mr. Comey’s firing even over Mr. Mueller’s objections.
Mr. Mueller’s need to navigate this complex landscape could explain the timing of the raid on Mr. Manafort’s house, which took place in the early hours of July 26. The raid came one day after Mr. Manafort was interviewed by staff members of the Senate Intelligence Committee.
On the day of the raid, Mr. Manafort was scheduled to talk to the Senate Judiciary Committee, an interview that was eventually canceled.
It is unusual for a prosecutor to seek a search warrant against someone who, like Mr. Manafort, had already put his lawyer in contact with the Justice Department. No search warrants were executed during the investigations by Mr. Starr or Patrick J. Fitzgerald, a special counsel appointed during the George W. Bush administration to investigate the leak of the name of a C.I.A. officer.
To get the warrant, Mr. Mueller’s team had to show probable cause that Mr. Manafort’s home contained evidence of a crime. To be allowed to pick the lock and enter the home unannounced, prosecutors had to persuade a federal judge that Mr. Manafort was likely to destroy evidence.
Said Mr. Gurulé, the former federal prosecutor, “Clearly they didn’t trust him.”