"Given what was being said publicly, the Special Counsel would have been remiss to ignore such an obvious potential link between the Trump campaign and the Russian government", Jackson wrote.
Peter Carr, a spokesman for the special counsel's office, declined to comment.
"The appointment order here purports to give the Special Counsel power to investigate a specifically identified matter and anything that arises in the course of the investigation, without further consulting or obtaining approval from the Attorney General or Acting Attorney General", a filing by Manafort's lawyer read.
The charges Manafort faces in D.C. include money laundering and conspiracy to defraud the United States. On May 4, Ellis ordered Mueller's prosecutors two weeks to provide "completely unredacted versions of [Deputy Attorney General] Rosenstein's orders assigning special counsel Mueller" before he would make a decision on keeping the Manafort indictment or dismissing it. He has also argued that Mr Mueller's case against him has nothing to do with Russian interference in 2016 election, and that the probe by the Federal Bureau of Investigation into his Ukraine dealings predates the Russia probe.
Citing Manafort's years of work in Ukraine, his prominent role on the Trump campaign and his publicized connections to Russian figures, Jackson said it was "logical and appropriate" for Mueller's team to scrutinize him as part of their investigation into Russian election meddling and possible coordination with Trump associates. He has pleaded not guilty in that case, as well as in the charges that included bank fraud and tax fraud that were brought against him in Virginia.
USA district judge Amy Jackson declined to throw out the case against Manafort, who faces two indictments from the special counsel. And Donald Trump cited them in a speech to the National Rifle Association to claim that Mueller's indictment is a "phony Russian Federation witch hunt".
So the charges in Jackson's courtroom will proceed against Manafort, and they will be prosecuted by Robert Mueller. The memo shows Rosenstein authorised Mueller to investigate Manafort's Ukrainian work and related financial crimes.
Judge Ellis, who was appointed to the bench by Republican president Ronald Reagan, has also said he too wants to see an unredacted copy before he can fully form a decision on whether to dismiss the charges.
Earlier this month, Judge T.S. Ellis, a federal judge in Virginia, questioned the scope of Mueller's investigation, at times warning against "unfettered power" and calling attention to the fact that charges against Manafort predate his time on the Trump campaign.