A Herald investigation can reveal senior roads officials raised multiple warnings about the elevated Skytrain section of the Sydney Metro North West project, months before large concrete spans on what is effectively Australia's longest bridge started to buckle and crack.

"Roads and Maritime's primary concerns relate to construction, including quality assurance, which in turn raise issues of structural reliability and public safety," the agency's chief executive was warned in a briefing drafted by the office of acting chief operating officer Angus Mitchell only four months ago.

Yet repeated warnings from the senior managers at NSW's roads agency, as well as alarm bells raised by the project's independent certifier in the months leading to his resignation in September, failed to convince sections of the state's transport bureaucracy responsible for building the rail project.

The fears about the structural soundness of the 4.5-kilometre viaduct, over which driverless passenger trains will run every two minutes, are revealed in hundreds of pages of internal government documents and emails obtained using freedom of information laws.

The Skytrain, which runs through the north-west suburbs of Kellyville, Bella Vista and Rouse Hill, has been plagued by design problems, cost blow outs and delays since construction started in 2014. The Herald has previously reported that sections of the elevated rail line have had to be replaced or strengthened due to cracks and buckling in long concrete spans.

But some of the strongest concerns, it can be revealed, have been raised by RMS, whose managers resisted giving approval for construction of the viaduct over roads. The Skytrain's route runs above some of the busiest roads in the city's north-west, including Windsor Road.

In a briefing written for RMS chief Ken Kanofski​ in early September, Mr Mitchell laid bare the roads authority's concerns about the project.

"These concerns include public safety and the viaduct's structural integrity, as well as a lack of independent certification, and non-compliance with conditions," Mr Mitchell's briefing says.

The briefing says RMS's manager on the project believed Sydney Metro, the government body overseeing construction of the viaduct and the rest of the 66-kilometre rail project, had not given "adequate assurance that the project meets [works authorisation deed] requirements".

"The independent certifier has raised similar concerns," the briefing says.

Two weeks after that warning in September, the viaduct suffered its most serious failure yet. A large concrete span buckled due to a combination of failings in the construction process, forcing work on the viaduct to be halted immediately.

"The scale of the incident is very substantial with an entire viaduct span at risk," a RMS manager warned in an email a day after the buckling.

The viaduct section – including a 270-metre cable bridge over Windsor Road – of the Sydney Metro project has been touted as a landmark element of Australia's biggest public transport project.

An Italian consortium, Salini Impregilo, won the $340 million bid to build the viaduct. In 2014 the then prime minister of Italy, Matteo Renzi, even appeared at a ceremony in Kellyville to inspect early works.

But the documents obtained by the Herald show that, less than a year later, RMS started to seek assurances from Transport for NSW that cracking in the overhead spans would not place motorists at risk.

In November 2015 RMS's manager on the project, Anthony McMahon, warned in an email that "the critical path for the entire project is at risk" if a squabble between the Italian contractors and Transport for NSW was not resolved.

The Herald then revealed in January last year that two of the viaduct's spans had suffered cracking.

By May 2016, concrete slurry had started to fall from a section of the viaduct over Memorial Drive in Rouse Hill. The slurry fell onto four cars after one span suffered cracking.

"Each person was subsequently contacted by [the Italian contractors], and offers to wash and detail their cars were accepted," the project team said in an email to RMS.

At the same time, the independent certifier was also detailing a long list of concerns about the project, including that Transport for NSW had failed to prepare a required inspection and test plan. An independent certifier provides crucial oversight for a project by ensuring it complies with construction and design standards.

Sydney Metro's deputy project director, Khalil Mansour​, later refuted the independent certifier's claims in an email to RMS.

The RMS was so troubled by the potential risks that its manager on the project told Sydney Metro in an email on May 27 that the agency could not approve construction until Transport for NSW "demonstrated that the current viaduct structural integrity issues and recent safety incidents will not expose any RMS asset or asset user to risk".

In another email to Sydney Metro 11 days later, Mr McMahon said the roads authority was "concerned that the current quality management plan and management procedures do not sufficiently demonstrate" that standards were being met.

A day after that email, Transport Minister Andrew Constance told a press conference  there was no danger of the Skytrain project failing to meet its deadline for completion of the first half of 2017.

"This project is on time, and it's on budget," he said at the time.

Yet six days later, Mr McMahon emailed his colleagues at RMS to tell them that Transport for NSW had initially attempted to gain approval for construction without any assurance that "their contractors' mitigation proposals were adequate" or that risks to roads were considered "despite lessons learned from the previous incident".

In an apparent sign of the pressure on RMS to approve construction over White Hart Drive, the briefing from the agency's acting chief operating officer in early September reveals that Sydney Metro had "indicated that they will escalate the matter if approval is not forthcoming given key project delivery risks they face".

Mr Mitchell's briefing also shows that Transport for NSW, which has repeatedly said that "safety is our number-one priority on Sydney Metro", gave assurances that it had "matters in hand and that the safety of road users and assets was protected", only for subsequent cracking to raise "fresh concerns".

"In addition, there has been no progress certification from an independent certifier for any of the works completed within the past two years and many records exist that identify issues with [works authorisation deed] quality compliance," it says.

Just before Christmas, Transport for NSW released a report it commissioned into the buckling of a span in September, which found a combination of failings in the construction process.

Following the report, Sydney Metro project director Rodd Staples said the incident was "very disappointing" and it had made that position clear to the contractor.

"But our focus has been to learn the lessons from it and to put actions in place to make sure that it doesn't occur again," he said last month.

A Sydney Metro spokesman said all of the work on the Skytrain over public roads had been with RMS's authorisation to "ensure that safety and compliance measures are in place".

"The Sydney Metro Delivery Office has always acted consistently with its obligations and proactively addressed any issues which have arisen in its dealings with all relevant parties, including Roads and Maritime, Skytrain builder Salini Impregilo and Skytrain independent certifier Arcadis," he said in a statement on Friday.

"The Skytrain structure over public roads is regularly inspected by Transport for NSW as part of the ongoing construction and quality assurance process."

Arcadis continued to certify completed sections of the Skytrain in accordance with the requirements set out in contracts, he said.

The Skytrain is part of the $8.3 billion first stage of Sydney's new metro rail line from Rouse Hill in the north-west to Chatswood, which the government wants to open in 2019, the year of the next state election.

The second stage of the line from Chatswood, under Sydney Harbour, the CBD and onto Sydenham and Bankstown in the south west, is scheduled to open in 2024 at a cost of up to $12.5 billion.