Mr Justice Scott-Baker said there seemed to be a "conflict between profit and safety" at GWT, which has made no financial provision for the crash in which seven passengers were killed and 150 injured.
According to its latest returns, GWT paid out pounds 24m in dividends to shareholders, but set nothing aside for any fine the court might impose and had failed to create any separate fund for safety.
The man who bore the brunt of the judge's anger was Richard George, the managing director of Great Western at the time of the disaster. Mr George did not appear in court yesterday on the day the company admitted putting passengers at risk.
When Mr Justice Scott-Baker asked defence lawyers if Mr George was in court to answer questions, he was told no. The judge replied: "He is the man in charge of safety, yet he is not here. He has not taken the trouble to come to court.
"I was told on more than one occasion that he was the man in charge of safety and one would have thought he would have come to court to hear what was said on behalf of Great Western Trains."
A GWT spokesman said Mr George had spent the morning preparing submissions for a public inquiry, due in September, into the crash, that he took the matter very seriously and that he would attend the court if asked to do so.
Corporate manslaughter charges against GWT were dropped three weeks ago because the judge ruled they could only be successful if Mr George had personally contributed to the crash. Instead the company yesterday pleaded guilty to an offence under health and safety legislation whereby it acknowledged it exposed passengers to danger. The offence carries an unlimited fine.
The company and prosecution lawyers later clashed over where the blame lay. Jonathan Caplan, QC for the company, said the driver, Larry Harrison, 57, had not operated the train as he was trained to do. An earlier hearing was told that Mr Harrison had been packing his bag when the express ploughed into an empty freight train in September 1997, having passed through two red lights. Manslaughter charges against Mr Harrison had also been dropped, partly on health grounds, a decision that angered relatives of some of the victims.
For the prosecution, Richard Lissack QC pointed out that the company had admitted it was at fault by allowing the train to leave Swansea at a time when two of its safety devices were not in operation. However, Mr Caplan said failure to stop the train was a contributory factor and not a "significant" cause of the disaster, a contention "utterly rejected" by the Crown.
Mr Justice Scott-Baker said: "The consequences of the driver missing a red signal at 120mph are so dreadful, it seems to me common sense there has to be some kind of back-up."
Mr Lissack said less than two weeks before the crash Mr George had made a policy statement at a safety committee, saying: "I wish to ensure that ... unsafe acts and hazards are identified and corrected."
The court heard that the Paddington-bound train, carrying about 200 passengers, passed through Hayes and Harlington station at around 125mph. Two minutes later it collided with the freight train.
Mr George, who was in one of the first-class compartments that took most of the impact, was commended for helping the injured to safety.
The hearing continues.