Prosecutors said the financier made two payments, one for $100,000 and another for $250,000, to a pair of suspected co-conspirators, who were not named.
The allegations were made in a court filing asking that Epstein be denied bail while he awaits trial.
Epstein is scheduled to be in court Monday morning for a bond hearing.
His lawyers have not yet commented on the payout claims.
The former hedge fund manager - who was arrested last week on child sex trafficking charges - doled out a total of at least $350,000 to two people past year, federal prosecutors said in new court papers. "I wasn't sure at the time who dropped the ball or failed to do what they had to do", Garcia said.
"Neither of these payments appears to be recurring or repeating during the approximately five years of bank records presently available to the government", they said.More news: NY power outage knocks out subways, businesses, elevators
"This course of action, and in particular its timing, suggests the defendant was attempting to further influence co-conspirators who might provide information against him in light of the recently re-emerging allegations", Berman wrote.
Epstein became arrested on 6 July and has been charged with intercourse trafficking and conspiracy.
"In this way, Epstein created a vast network of underage victims for him to sexually exploit, often on a daily basis", the U.S. Attorney's Office for the Southern District of NY said in a news release.
In a 50-plus-minute lawyerly rebuttal, he argued his office had secured the best deal it could and had worked in the best interests of Epstein's victims.
They cited his payments to possible witnesses and the risk that he would flee as reasons to keep him in jail, while describing him as "unrepentant and unreformed".
President Donald Trump, accompanied by Labor Secretary Alex Acosta, right, speaks to members of the media on the South Lawn of the White House in Washington, July 12, 2019.
Why did Mr Acosta step down? Similar charges filed against Epstein by federal prosecutors in NY this week had put Acosta's handling of the 2008 agreement with the now-jailed financier back in the spotlight.More news: Ex-Red Sox slugger David Ortiz recovering from 3rd surgery
Mr Acosta was then the US Attorney in Miami and oversaw the non-prosecution deal with Epstein, which allowed the financier to serve 13 months in jail - with much of that time spent on work release at his Palm Beach office. The deal came under scrutiny earlier this year after reporting by The Miami Herald. Acosta announced on Friday that he would step down from President Donald Trump's cabinet, saying he didn't want to distract from the strong economy.
Prosecutors' filing Friday was a response to defense attorneys request that Epstein be let out on bail before his trial.
However he added: "It may per chance per chance per chance per chance even be egocentric for me to defend in this quandary and continue talking about a case that is 12 years weak".
"Mr. Acosta will now have plenty of time and no distractions that prevent him from fully accounting for the sweetheart treatment Epstein received", he said.
Mr Trump, former president Bill Clinton and Britain's Prince Andrew had all previously been members of Mr Epstein's social circle over the years.
In a 2002 profile in New York Magazine, Mr Trump referred to Epstein as a "terrific guy". 'He's a lot of fun to be with.
Acosta's departure, continued Thomas, "should only be the beginning: we need to hold all the powerful people that engage in or enable sexual abuse accountable".More news: United Kingdom police investigate Kim Darroch cables
Stories of Epstein's present wealth fluctuate, alongside with his Virgin Islands-primarily primarily based agency generating no public records.