Some 10,000 rescue workers and police officers are suing New York City, saying they suffered health problems working in the dust and debris.
Federal Judge Alvin Hellerstein said that he did not think the agreement represented a sufficient sum of money.
He said further negotiations were needed for a fair deal.
Lawyers' fees
Mr. Hellerstein said the injured workers should be able to know the approximate value of the cash award they might receive before deciding whether or not they should accept the settlement.
"I will not preside over a settlement that is based on fear or ignorance," the judge said.
He added that he was concerned that too much of the final sum would be eaten up by legal fees.
Under the current deal, lawyers' fees may be drawn from a $1 billion fund set aside by federal government to cover the claims.
The fund was set up after the attacks when New York City was unable to find private insurance to cover claims originating in the clean-up effort.
The deal, announced just over a week ago, requires 95% of plaintiffs to accept it in order for it to go ahead. Workers were given just 90 days to decide whether they wanted to take part.
The judge said this was not enough time for the plaintiffs to make a decision of such importance.
The deal had taken years to negotiate and was announced some two months ahead of the first trials.