"Although Mr Harrison bears a heavy responsibility for the Southall accident, there is compelling evidence of serious failings within Great Western Trains, his employers," he said.
Mr Burnett was speaking on the closing day of the inquiry into the crash in which a high- speed train operated by Great Western Trains (GWT) from Swansea to Paddington went through a red signal in Southall, west London, in September 1997, colliding with an empty freight train, killing seven passengers and injuring 150 others.
In his submission, Mr Burnett highlighted the failure of the automatic warning system (AWS) equipment in the train and the "non-use" of the automatic train protection system (ATP).
The fault in the AWS had been noted the evening before the crash, he said, and had re-curred at Paddington the following morning. The train should have been "turned" at Swansea, so that the power car with functioning AWS led on the way back to London.
Mr Burnett said he believed Great Western Trains had been informed about the defect but had not acted upon it. He added that the Great Western main line between Bristol and Paddington was fitted with ATP, but at the time of the accident it had not been turned on.
"The detailed investigation of GWT which the Southall accident has spawned reveals an organisation which was seriously under-performing to the detriment of the safety of its customers," he said.
Jonathan Caplan QC, for GWT, said the company accepted it was at fault at the time of the disaster. But he added that the rail industry in general had failed to appreciate the importance of the early warning system and GWT was no exception.
John Hendy QC, acting for some of the passengers and bereaved families, called for ATP to be fitted and operated across the railway.
Anthony Scrivener, QC, acting on behalf of Mr Harrison, said: "Mr Harrison was required to drive a high-speed train on line speed with AWS isolated - no one at this stage appreciated the danger involved in doing so, least of all Mr Harrison, who had never been warned or even trained to drive a train in that condition.
"In the opinion of experts if AWS had been working, it is most probable that the accident would not have taken place."
The closing day of the Southall inquiry was held the day before preliminary hearings were due to begin into the Paddington rail crash of two months ago.