Network Rail said it "let down" passengers when engineering work overran causing disruption to thousands of travellers over the New Year period.
Engineering work at Rugby caused delays for thousands
Work on the West Coast Main Line at Rugby and Nuneaton was delayed and London's Liverpool Street station was also shut for longer than planned.
A report published by Network Rail said it would use its own staff in future rather than relying on contractors.
Chief executive Iain Coucher said: "I'm determined it won't happen again."
The report also said contractors who continue to work for Network Rail would also be expected to rely less on agency staff.
It added that both projects had been deliverable, but poor productivity and poor manpower supervision led to the delays.
The Network Rail investigation has run in parallel to one started by the Office of Rail Regulation (ORR).
The ORR's findings are expected to be published at the end of February.
Network Rail's report also said the company would establish "military-style command posts" for all future major works to provide clearer lines of authority.
Mr Coucher said: "We invested almost £125m in the railway during the Christmas holidays aimed at improving train services. Over 1,000 pieces of work were undertaken and all but three went well. That is three too many in our book.
"We let passengers and freight users down and I'm determined that it won't happen again. That is why we will be taking these far-reaching and decisive measures in the weeks and months ahead."
The work on the West Coast Main Line at Rugby and Nuneaton in Warwickshire closed a 40-mile section of the line and passengers were forced to take buses between Birmingham and Northampton.
Engineers should have finished by the end of 30 December, but Network Rail, which used contactors to carry out the repairs, said it needed another day to complete the £415m job.
Work was not finished for a further three days, with full services not returning until 4 January.
There were also problems on services run by the One train company, with Liverpool Street station having to remain fully closed for about half a day more than was originally planned.
Opposition MPs, business leaders and passenger groups have condemned Network Rail's handling of the engineering work.
Gerry Doherty, general secretary of the Transport Salaried Staffs Association, said: "This has been a spectacular example of the private sector failing to deliver on a public transport project.
"We welcome Network Rail's attempt to avoid a repeat of this fiasco, but we don't think they go far enough. We would like to see renewal work brought back in-house so NR can get a proper grip on these key projects."