Ministers are considering a new scheme that would see a 1.5-mile tunnel built under the Chiltern Hills, at an additional cost of £500m.
Campaigners have opposed the proposed HS2 route because of its impact on the environment, and the government is hoping the use of a tunnel through an area of outstanding natural beauty will help head-off opposition.
The delay is unlikely to affect the overall timing of the programme's delivery, with the bill unlikely to become law until 2013, with construction work expected to start in 2015.