The Deputy Prime Minister responded angrily to MPs who accused his department of setting targets at whim and making little impact, saying the criticisms were "ill-founded."
And he insisted that the new Train Protection and Warning System (TPWS), to be fitted across the network before 2004, would "save lives and reduce accidents."
The safety system aims to prevent accidents such as the Clapham rail disaster, which killed 35 people and injured 500 in 1988, by automatically stopping trains if they pass a red danger signal.
The TPWS is a much cheaper alternative to the more sophisticated system recommended by Sir Anthony Hidden QC, who chaired the inquiry into the Clapham disaster He called for an Automatic Train Protection (ATP) system to be fitted within five years. But at a cost of pounds 1bn, that was judged too expensive.
Mr Prescott, who recently experienced his most bruising weeks in office, said he was "increasingly concerned" over the number of trains going through red signals - 593 last year.
The new system, combined with phasing out old slam-door carriages used by thousands of London commuters, would give passengers the "safe, comfortable and reliable service they deserve".
George Muir, the director of the Association of Train Operating Companies, said the timetable for installing TPWS was "challenging, but train operators have made this project a priority".
But the Tories accused Mr Prescott of trying to "repair his damaged reputation by deceit" because the TPWS had only completed its trials last year and had therefore not been an option for the last Government.
Jimmy Knapp, the general secretary of the largest rail union, the RMT, welcomed the move, but said: "This additional protection must not be at the expense of other much-needed rail investment."
Mr Prescott angrily dismissed a report from the Labour-dominated Select Committee on the Environment, Transport and the Regions, which last month attacked the department for doing little but publish policy documents. He said the committee ignored progress being made and insisted that targets were being underpinned by programmes of work.
"I was sorry the committee's report made sweeping criticisms of the department but failed to back them up with hard facts," he said.
"It failed to recognise the substantial progress my department had made towards delivering real improvements to the quality of life in this country. The response I have published today sets the record straight.
"A number of the committee's conclusions and recommendations, for example those relating to objectives, targets and achievements, fails to take account of the evidence made available."