The legal documents or information requests similar to a subpoena were delivered to Toyota on Tuesday and the company has 30-60 days to respond or face fines.
The agency, part of the US Department of Transportation, said it "is requiring Toyota to provide documents showing when and how it learned of the defects affecting approximately six million vehicles in the US alone".
"Safety recalls are very serious matters and automakers are required to quickly report defects"
US transport secretary
"Safety recalls are very serious matters and automakers are required to quickly report defects," Ray LaHood, the US transportation secretary, said in the statement on Tuesday.
Calling the company "a little safety deaf", LaHood vowed "to hold Toyota's feet to the fire" to make sure it follows through on promises to make their vehicles safe.
US federal law requires all auto manufacturers to notify the NHTSA within five days of determining that a safety defect exists and promptly conduct a recall.
Investigators will probe how the manufacturer learned of the defects in the recalled Toyota and Lexus vehicles, such as via consumer complaints or factory testing, and when the problems were discovered, said the agency.
If found in violation of US safety rules Toyota could face up to $16.4m in fines.
In response to the NHTSA request, Toyota said it took "responsibility to advance vehicle safety seriously and to alert government officials of any safety issue in a timely manner".
"We are reviewing NHTSA's request and will cooperate to provide all the information they have requested."
In recent months Toyota has recalled millions of vehicles worldwide due to problems linked to accelerator and brake functioning that have sullied the company's safety reputation.
The detailed US request for information came a day ahead of a scheduled news conference by Akio Toyoda, the company's president, on the progress of the massive recalls.
Toyoda, the grandson of the Toyota founder, has previously offered public apologies and plans to fly to the US, where the company faces a congressional grilling on February 24 and a host of lawsuits.
In a related development on Tuesday, Toyota said it was suspending production briefly at two plants, in Kentucky and Texas, over concerns the recalls could lead to big stockpiles of unsold vehicles.
Commenting on the US information request Rebecca Lindland, an analyst at IHS Global Insight, said the NHTSA itself was in the crosshairs of critics alleging it had failed to properly oversee auto safety.
"They're under a lot of pressure to see what Toyota is doing," she told AFP. "It is not surprising to see they're getting more aggressive."