NASCAR announced the confiscation just two days out from the prestigious Daytona 500.
RFK dominated the Daytona Duels yesterday, with its drivers Brad Keselowski and Chris Buescher completing a cleansweep to lockout the second row for the main event.
Team Penske's quartet was led by Austin Cindric, who is due to start the 500 from fifth, ahead of team-mates Ryan Blaney (seventh), Harrison Burton (eighth) and Joey Logano (20th).
What the technical investigation means for both teams and its drivers is not yet clear, with competition officials indicating the confiscated wheels will be sent to NASCAR's Research and Development Centre in North Carolina.
Any potential penalty will be determined after the inspection is finalised.
NASCAR's toughened penalty structure for violations does include the ability to revoke playoff eligibility.
The Daytona 500 is the first points event for the new Next Gen cars, which run on 18-inch aluminium wheels.
Hendrick Motorsports' Kyle Larson and Alex Bowman will share the front row for the race start on Monday (Australian time).