"The federal government will initiate an unscheduled expenditure to ensure that October salaries are paid on time," the ministry spokeswoman said.
The trade union Verdi on Tuesday said that local staff have continued being paid during past US government shutdowns, but expressed fears that the current Trump administration appeared likely to halt paycheques.
READ ALSO: Workers union demands pay for German workers caught in US government shutdown
The union contended that doing so would be a clear violation of German law, and urged a solution to prevent any missed pay.
The finance ministry spokeswoman said it currently remains unclear whether US payments might still come through despite the shutdown.
But the federal government in Berlin and the German state of Rhineland-Palatinate struck the deal to guarantee salaries will be paid and avoid any issues, she said.
The German government anticipates being reimbursed for the payroll cost once the US side makes payment, according to the spokeswoman.
Berlin's contribution is "a sign of solidarity with the US armed forces stationed in Germany and their civilian employees", she added.
Germany hosts tens of thousands of US military personnel locations including the Ramstein Air Base, which serves as a US Air Force headquarters for Europe and Africa.
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