The administration has awarded $67 million in navigator grants to 105 organizations.
Energy and Commerce Republicans, in their letters to grant recipients, sought copies of all communication with the administration and raised questions about whether navigators could steal personal information or use their contacts for political activities.
Waxman, the top Democrat on Energy and Commerce, said the investigation was baseless.
"There is no legitimate predicate for these letters and no evidence of any malfeasance from any of the organizations," he wrote in a letter to Energy and Commerce Chairman Fred Upton (R-Mich.) "It is an abuse of your oversight authority to launch groundless investigations into civic organizations that are trying to make health reform a success."
Upton's letter requested that navigators turn over all of their records and schedule in-person briefings by Sept. 13. Open enrollment in the healthcare law's exchanges begins Oct. 1.
"It appears that these requests may have been sent solely to divert the resources of small, local community groups, just as they are needed to help with the new health care law," Waxman wrote.