In a letter to GM, NHTSA said the automaker had been fined $28,000 so far and would be subject to daily fines until it answers all 107 questions the agency asked in its investigation.
The agency is probing why the automaker waited until February to order a recall despite first learning of the defect more than 10 years ago.
At least 13 deaths in Saturn Ions, Chevrolet Cobalts and other models have been linked to the faulty ignition switches, which can cause the engine to turn off suddenly, disabling the air bags and making steering and braking more difficult.
GM said in a statement it had "fully cooperated" with NHTSA. The automaker said it had sent more than 271,000 pages of documents to the agency and would provide additional documents "as soon as they become available."
The NHTSA said the automaker had not responded to over a third of its questions by the April 3 deadline. The 17 pages of questions were submitted to GM on March 4.
Many of the questions seek to track who in GM knew about the defect and when. GM CEO Mary Barra, who testified last week to two congressional panels investigating the recall, has said she did not learn about faulty switch until January 31.
NHTSA said GM had informed the agency on March 20 it would not be able to respond to all the technical engineering questions by the deadline.
"NHTSA had no objection to GM taking additional time to respond to technical engineering questions, with the understanding that GM would fully respond to the remaining requests by the April 3 deadline. GM failed to do so," NHTSA Chief Counsel O. Kevin Vincent said in the letter.
NHTSA said GM had also told the agency it was not able to respond fully because of an investigation into the recall by former federal prosecutor Anton Valukas, who has been hired by GM to conduct an internal probe.
Vincent said if GM did not fully respond to NHTSA's questions "immediately and pay all civil penalties," the agency may refer the matter to the Justice Department.
NHTSA has said GM's responses to the questions would be made public once the agency's lawyers had a chance to review the documents and redact any confidential information.
The US agency itself is being investigated by the two congressional panels and the Transportation Department's inspector general for missing the defect.