The timetable for planning phase one of the HS2 project - from London to Birmingham with work due to start in 2016/17 - was "challenging", the National Audit Office report said.
This challenging timetable "makes delivering this work difficult and increases the risk that the programme will have a weak foundation for securing and demonstrating success in the future", the report said.
Expressing "reservations" about the business case for HS2, the NAO said the Department for Transport's (DfT) methodology for appraising the project put a high emphasis on journey-time savings, from faster and more reliable journeys.
But the report added that the relationship between these savings and the strategic reasons for doing the project, such as rebalancing regional economies, was unclear.
The NAO said it was also unclear whether the business case covered just phase one or the full route including phase two - the Y-shaped network from Birmingham to Manchester and Leeds due to open in 2032/33.