The Justice also denied a similar emergency request filed by lawyers on the girl's behalf.
All emergency requests are submitted to a circuit justice, rather than to the full Court.
Congressional Republicans are divided on whether to add a few billion dollars more to the emergency request, or many billions.
Administration officials said later that this emergency request would total about $2 billion.
He also said the commission would rule by Jan. 1 on an emergency request for a temporary rate increase of 5.4 percent.
Justice Kennedy referred the emergency request to the full Court.
The case was handled as an emergency request, and a decision would be handed down two days later.
At that time, it expects to submit another emergency request for money.
Usually such emergency requests are provided on top of money already appropriated to the Pentagon budget.
The Chief Justice turned down an emergency request by opponents of the business agreement.