But in a statement, the Fed argued for letting the programs continue.
The announcement could signal potential trouble for the incoming Biden administration.
Futures contracts for the Dow Industrials and S&P 500 fell 0.7% Thursday evening.More news: Hair Dye Seemingly Drips Down Rudy Giuliani's Face During Bizarre Press Conference
Mnuchin has approved a 90-day extension for a group of Fed facilities that aren't connected to the CARES Act funds passed in March.
But Fed officials have emphasized in recent days that the broad economy is not yet out of the woods, with the pandemic spreading, millions unemployed and important business sectors suffering Depression-level downturns.
Mnuchin in his letter nodded to "the unlikely event that it becomes necessary in the future to reestablish any of these facilities", saying that any Treasury chief would be able to use other rainy day funds under the control of the department or could get additional funding from Congress.
The programs, particularly the "Main Street" and local government landing programs, raised the prospect of trillions of dollars in central bank credit flooding into an economy that had been partially shut down in the spring because of the pandemic. "I've made that decision, we've made that decision, and you'll hear that either just before or just after Thanksgiving", Biden said. The Municipal Liquidity Facility had only issued about $1.7 billion in loans.More news: California Medical Association officials attended French Laundry dinner party with Gavin Newsom
But the programmes were considered an important element of the pandemic response, broadened at the behest of lawmakers who wanted the central bank's lender-of-last-resort powers, usually limited to financial institutions, opened to the entire economy because of the pandemic's dramatic impact on commerce. Republicans and Democrats have been deadlocked for months on approval of another round of coronavirus support measures. Many progressive economists have argued that a Democratic-led Treasury could support the Fed taking on more risk and making more loans to small and mid-sized businesses and cash-strapped cities under these programs.
Mnuchin's decision added to market anxiety about broader economic growth as data shows the early fast recovery from a historic plunge in the US economy is fading, with more than 10 million who had jobs in January still out of work. "These facilities, which were established in response to the unprecedented market turmoil caused by the COVID-19 pandemic earlier this year, have successfully achieved their intended goal".
A senior Democratic aide told Reuters there had been a mid-afternoon meeting on Thursday among congressional aides that discussed coronavirus relief and efforts to pass a $1.4 trillion bill to keep government agencies operating beyond December 11 when current funding expires. "How many times will Washington trip on its shoelaces in response to this crisis?"More news: Covid-19: Twins delivered in Birmingham while mother in coma