The current performance was "unacceptable", said Mike Grant, the rail franchise director, whose office published the figures. Just one company, the small Isle of Wight Island Line, was given the top grade for performance.
Richard Branson's Virgin West Coast and Virgin CrossCountry train companies were among operators whose performance has deteriorated.
The figures disclosed that, of the routes operated by the 25 train companies, 25 routes showed an improvement in reliability, 36 declined and 16 stayed the same in the year to 31 March, 1999, compared with the previous 12 months.
On punctuality, 21 routes improved, 54 declined and 2 remained the same.
Taking just the last quarter of 1998-99, reliability improved on 19 routes, declined on 33 and stayed the same on 25.
Last-quarter figures for punctuality showed 27 routes improved, 48 declined and 2 stayed the same.
Mr Grant said: "In too many cases, performance is not acceptable. While passengers can be reasonably confident their train will run, the operators' record on ensuring they get there on time remains unacceptable."
Sir Alastair Morton, chairman of the shadow strategic rail authority, said: "What is emerging is a premier league of still only a few train operators, improving the capacity and performance of gradually improving assets. The remainder may be first or second division - they need to raise their game."
Taking the 12 months ending 31 March 1999, only Island Line reached category A by achieving at least 95 per cent punctuality and 99.5 per cent reliability on services.
Six companies were in category B - achieving 90 per cent punctuality and 99 per cent reliability.
Twelve were in category C, with 85 per cent punctuality and 98.5 per cent reliability, while three fell into category D, with 80 per cent punctuality and 98 per cent reliability. In category E were Silverlink, Cardiff Railways and CrossCountry, which achieved less than 80 per cent reliability and less than 97.9 per cent reliability.
Companies' placings in the categories depended on which of its reliability and punctuality performances was the poorer. Although CrossCountry had a B for its reliability, it received an E for punctuality.
Operators that achieved overall category improvements were Midland Main Line (B), Great Western (C), and Connex South Eastern (C).
Operators that declined were CrossCountry, Cardiff Railways, Great Eastern (C), Gatwick Express (C) and West Coast Trains (D).
Mr Grant said: "This underlines the challenge the industry faces if it is to deliver improvements promised at February's national rail summit."
The pressure group Save Our Railways said the figures were "proof positive a fragmented railway does not work".
Jonathan Bray, campaigns director, said: "Passengers' patience is running out. They want to see the Government give rail regulators the powers they need to turn the railway around."Reuse content