The Major Projects Authority (MPA) has given 32 projects a red or amber/red rating, meaning they are deemed unachievable or in doubt.
Red projects include two £7bn aircraft carriers dogged by delays.
The Cabinet Office welcomed the report and said it would lead to improvements.
The MPA was established in 2010 in a bid to turn around the civil service's "lamentable record" of delivering large schemes.
Its report warns that billions of pounds of public money could be at risk because of delays and inefficiencies in delivering key projects.
BBC News - Warnings over flagship projects