Whalley has been taken into police custody in connection with the same incident which saw striker Ricky Miller arrested on Monday.
Miller, also suspended by the Hatters, has since been released on bail.
A club statement read: “Following yesterday’s club statement regarding Ricky Miller, Luton Town Football Club can confirm that Shaun Whalley has been placed in police custody in connection with the same alleged incident in the early hours of Monday morning.
“As a result, Shaun has also been suspended by the club, pending a police enquiry.
“An internal investigation at Kenilworth Road continues and Luton Town can place on record once again that any player guilty of misconduct will be disciplined appropriately.
“Meanwhile Bedfordshire Police have released a statement today [Tuesday] confirming that Ricky Miller has been released on bail until June 2.”