The U.S. Supreme Court on Monday dealt a major setback to lawyers for Nomura Holdings Inc., Royal Bank of Scotland Group plc and other financial institutions that argued that the National Credit Union Administration waited too long to sue over billions of dollars in allegedly shoddy mortgage-backed securities. But questions underlying the banks’ challenge still may not be fully resolved.

The high court denied a petition for certiorari lodged by a group of banks fighting the NCUA’s claims, which the agency brought in 2011 on behalf of federal credit unions that collapsed in the subprime crisis. The suit is one of several the NCUA, a government agency that supervises federally chartered credit unions, has filed against banks that allegedly hid the risks of mortgage-backed securities.