The government's official review into HS2 "strongly advises against cancelling" the project, the BBC can reveal.
It also says only building one section of the line which will link southern and northern England "doesn't make sense".
The BBC has read the full and final version of the report, which was led by former HS2 chairman Douglas Oakervee.
The government will announce its final decision on the scheme next month.
HS2 is designed to link London, Birmingham, Manchester and Leeds, cutting overcrowding on the railways and helping to rebalance the UK's economy.
But the project has faced criticism from both Labour and Conservative MPs for being over budget and behind schedule.
In the summer, the government commissioned an independent review on whether it should go ahead - although opponents later warned it would be a whitewash.
According to the review, the project could now cost up to double the official 2015 estimate of £56bn.
The review warns there is a "considerable risk" that the first phase of the project might need more money.
In the summer HS2 admitted the project was running around £30bn over budget and raised its overall estimate to £88bn.
But this review warns that the project might cost in excess of £100bn.
However, it strongly advises against cancelling it, saying HS2 would benefit the UK transport system and that there were no "shovel-ready" alternative upgrades to existing railways.
The review also says calls for just one section of the railway to be built to control costs would not be value for money.
And it says scrapping the scheme would have a detrimental impact on the UK's "fragile" construction industry.
It does express some caveats about HS2, though.
For example, it says the scheme will need to be properly integrated with other regional transport strategies - such as Midlands Engine Rail - to achieve economic transformation.
Work on Phase 1 is ready to begin so major alterations to that part of the scheme are not deemed possible. However, this report recommends doing more work on the plans for Phase 2 to ensure it is better value for money.
And it says further work is needed on understanding the potential impact of HS2 on homes and jobs.
Phase 1 of HS2 between London and Birmingham is due to open at the end of 2026, with the second phase to Leeds and Manchester scheduled for completion by 2032-33.
It is designed to carry trains capable of travelling at 250mph (402km/h).
On Wednesday, the chancellor threw his support behind the link despite the costs.
And BBC political editor Laura Kuenssberg said the mood music seemed to be pointing towards HS2 going ahead despite government nerves.
Major work has already been carried out at sites like Euston, Solihull and in central Birmingham. The project has already cost £9bn.
The government doesn't have to follow the recommendations of the review. However, it was personally commissioned by Prime Minister Boris Johnson and its emphatic endorsement makes scrapping the scheme even more unlikely.