It has also accepted that the cost will rise to HK84.42bn (£7.2bn) and agreed to defer any legal action until after the project is complete.
Mass Transit Railway Corporation (MTRC) had submitted its latest cost and time assessment to the government in June (link opens in new tab).
The Guangzhou-Shenzhen-Hong Kong Express Rail Link had been due to open in 2017 and had the cost had already been increased last year to HK$71.5bn from the original HK$65bn.
The revised cost is HK$880m less than MTRC had proposed in June, said secretary for transport and housing Professor Anthony Cheung. The MTRC has also agreed that it will bear and finance further cost overrun beyond the agreed level.
Cheung said the agreement does not mean the government is satisfied with the MTRC's performance as project manager, adding it may consider legal action over delays and cost overruns. However, in view of the extremely tight works schedule, the two sides have agreed to initiate such action only after the rail project's commissioning in 2018.