The pandemic-era programs, which are run by the Fed but use Treasury money to insure against losses, have provided an important backstop that has calmed critical markets since the coronavirus took hold in March. Removing them could leave crucial corners of the financial world vulnerable to the type of volatility that cascaded through the financial system in March. And by asking the Fed to return unused funds, Mr. Mnuchin could prevent Mr. Biden’s incoming Treasury secretary from restarting the efforts in 2021.

“The Federal Reserve would prefer that the full suite of emergency facilities established during the coronavirus pandemic continue to serve their important role as a backstop for our still-strained and vulnerable economy,” the central bank said in a statement.

The programs were backed by a $454 billion appropriation created as part of the government’s pandemic response package. Because of the way its emergency lending powers work, Jerome H. Powell, the Fed chair, needs the Treasury secretary’s signoff to make major changes to the programs’ terms. Extending the end date counts as a material change.

“I am requesting that the Federal Reserve return the unused funds to the Treasury,” Mr. Mnuchin said in a letter on Thursday.