There have been calls from Conservative MPs to scrap the high-speed line linking London to the Midlands and the North after costs ballooned, with some predicting the final price tag could rise to more than £100bn - almost double what was initially budgeted.
But in an interview with Sky News, the Prime Minister said that, while the project was a "mess", ministers would have to "keep digging".
"It's a colossal railway line. Now the truth is, the people who did it spent far too much money, they were profligate with the way they did it.
"They just wasted money," he told FYI, a news programme for children on Sky News.
"And the whole way it was managed was hopeless. So we're in a hole, we're in a mess. But we've got to get out of it.
"And we need a way forward, so we're thinking about how to sort it out now.
"In a hole the size of HS2, the only thing to do is keep digging."
It comes after Chancellor Sajid Javid threw his weight behind the high speed line, which advocates say would provide much-needed capacity on Britain's railways.
Mr Javid met with the PM and Transport Secretary Grant Shapps on Thursday, with those close to the Chancellor suggesting he was minded to back the scheme.
It is understood that, having reviewed costs and alternatives, the Chancellor, who represents a Midlands constituency, was set to "broadly back" the high-speed line from London to Birmingham, Manchester and Leeds.
Speaking before the meeting, Downing Street declined to rule out that Mr Johnson could overrule Mr Javid on the infrastructure project.
But Mr Johnson appears to be softening on his resolve following his most recent comments. A final decision is expected next month.
Mr Johnson has emphasised "levelling up" the regions through upgrades in infrastructure and HS2 supporters, such as former chancellor George Osborne, have said it would be "nuts" to cancel Europe's largest planned infrastructure project.
Whitehall's spending watchdog said this month that HS2 is over budget and behind schedule because its complexity and risks were under-estimated.
The National Audit Office (NAO) warned that it is impossible to "estimate with certainty what the final cost could be", but the final bill is expected to well-exceed the £56 billion set-aside for the build in 2015.
Meanwhile, several environmental groups say it would cause huge damage to natural habitats and ancient woodland.
Phase One between London and Birmingham was due to open in 2026, but full services are now forecast to start between 2031 and 2036.
A spokesman for HS2 Limited, the company tasked with its construction, said there was a "highly-skilled team in place" ready to start work on realising the full-scale of the plans if the PM gives the go-ahead.
"Since his appointment as CEO of HS2 Ltd in 2017, Mark Thurston has made several significant changes and improvements to the organisation, its governance and processes," said the spokesman.
"As the recent NAO report recognises, this work - along with a greater understanding of the ground conditions and build requirements - means ministers have the most robust cost estimates for Phase One of the HS2 project that they've ever had.
"If the Government decides to proceed, HS2 Ltd has a highly-skilled team in place ready to build Britain's new state-of-the-art, low-carbon railway."