Fewer than half the trains ran on time on some main line routes in the last 12 months, according to official figures.
Virgin Trains was only able to operate 48.9% of trains on time on the West Coast main line in the 12 months ending April 27 2013 while the CrossCountry company only managed a figure of 46.1%.
The statistics from Network Rail (NR) were based on "right time" performances in which trains are only regarded as being punctual if they arrive within 59 seconds of the timetabled time.
Under the 59-second rule, the NR table showed 68.0% of trains nationally were on time in the 12-month period ending April 27 this year.
Train companies below the average figure included Southern (55.5% punctuality), First ScotRail (59.8%) , East Coast (60.9%) and First TransPennine Express (63.8%).
Best-performing company was London Overground (86.8%) followed by Chiltern (86.5%).
NR also released regional figures for the four-week period ending April 27 based on the 59-second rule.
Overall, 72.3% of trains ran on time during this period, although long-distance operators only managed a figure of 58.0%.
NR also announced today the latest monthly punctuality figures based on commuter trains arriving within five minutes of the scheduled time and long-distance services arriving within 10 minutes of the scheduled time.
These are the figures on which rail regulators judge NR's performance and they showed that nationally in the period from April 28 to May 25 this year, 93.5% of trains were on time.
This compared with a figure of 92.3% for the same period last year.
Virgin Trains (85.7%), London Midland (89.2%) and East Coast (89.4%), were the only companies to fall beneath 90%, with the London to Tilbury and Southend company c2c being the best-performing company, with a figure of 98.2%.
NR said infrastructure, overhead line and signalling equipment problems caused the majority of delays on the West Coast Main Line during the period, thus impacting upon Virgin's punctuality.
It added that a series of measures to address performance on the southern end of the West Coast route would be announced in the next few weeks.
Later, NR produced more "right-time" figures - for the 12 months ending May 25 2013.
These showed that, nationally, 68.1% of trains ran on time under the 59-second rule, with the poorest-performing company being CrossCountry (46.3% on time) and Virgin Trains (48.9%).
The best-performing company was Chiltern (87.0%).
Under the 59-second rule, the number of trains that ran on time nationally in the period April 28 to May 25 2013 was 72.7% but only 60.2% of long-distance services were on time.
A spokesman for the Association of Train Operating Companies said: "According to the Government-set measure for punctuality, more than nine out of ten trains arrived as planned."