Hundreds of injuries to rail workers may not have been reported because of pressure and in some cases fear felt by staff if they give details of incidents.
The Rail Safety and Standards Board (RSSB) said there had been a "significant" level of under-reporting of injuries by Network Rail staff and those employed by contractors.
Its report said that between 500 and 600 injuries under the Reporting of Injuries, Diseases and Dangerous Occurrences Regulations (RIDDOR) might not have been reported over the five years between 2005/06 and 2009/10, mainly on infrastructure projects.
The report said: "The under-reporting of RIDDOR lost time injuries has occurred because of the change in both the culture of Network Rail and its relationship with its contractors since 2005. These changes are a result of the real and perceived pressure and, in some cases, fear felt by Network Rail staff and contractors if they report accidents or incidents.
"From the evidence gathered in the review, we consider this real and perceived pressure and fear have arisen as unintended consequences of the Network Rail implementation of the overall strategy for safety (which was consciously designed to improve safety), based on the use of quantitative safety targets, safety performance measures, league tables and contractual requirements linked to the number of reported RIDDOR lost time injuries, other management actions, such as the frequent company re-organisations and the application of a managing for attendance policy."
Other issues identified in the report included the procurement strategy used to drive down costs and improve efficiency, leading to the primary contractor companies making much greater use of temporary contract staff.
Network Rail directors, senior and local managers and frontline staff showed a real desire to improve safety, but there was some evidence that local managers were under such pressure to "get the job done" that it might, in some cases, lead to safety and safety reporting being "compromised", said the report.
The report said Network Rail should consider further steps to improve the working relationship between directors/senior managers and all levels of their staff and between the company and its contractors with a view to working towards a more "open and just" safety and reporting culture."
Anson Jack, RSSB's director of policy, research and risk, said: "This review highlights the unintended consequences of management initiatives intended to improve safety. It is the combination of Network Rail's internal and contracting culture together with quantitative targets, rather than just the targets themselves which created the under-reporting issue."
Bob Rixham, national officer of Unite, said: "Network Rail agreed to an independent review of how it reports staff accidents following intervention by Unite.
"The review exposes a culture where rail staff and contractors were under pressure not to report accidents. It's scandalous that directors shared £2.7 million in bonuses in 2010.
"Network Rail and the industry must now admit to themselves how bad the situation had become, and only then can the industry move forward and encourage and nurture a just safety culture."
Rick Haythornthwaite, NR's chairman, said: "I'm grateful to the RSSB for its work and to the Office of Rail Regulation and Unite for bringing this issue to our attention. While we can take some comfort from the report's clear conclusion that there was no link between under-reporting and executive bonuses, Network Rail needs to heed the lessons in this report if it is to achieve its ambition of a world class safety culture.
Peter Henderson, NR's acting chief executive, said: "Enhancing the safety of the railway and establishing a more open culture is a complex issue. To achieve our safety ambitions, we will work together with our contractors, unions and other stakeholders and use these findings to help develop a wide-ranging safety plan."
Ian Prosser, the Office of Rail Regulator's director of railway safety said: "We welcome the report RSSB has completed on behalf of Network Rail's board. It confirms the practice of under-reporting RIDDOR reportable injuries in Network Rail that we had raised early last year and subsequently made public in our annual health and safety report in July.
"The report's findings also reinforce the need for improving the underlying health and safety culture within Network Rail and its contractors so that they learn from all incidents. This has already been recognised by the company, which has made significant efforts since last summer to address the issues.
"The company still has some way to go, but building on their recent improvements I am now confident that the new leadership understands the problems and is clearly focused on improving its health and safety culture. It is important that the change spreads through the procurement process to contractors too."