Five months into their Old Bailey trial, Mr Justice Mackay ordered the jury to find the executives not guilty.
A corporate manslaughter charge against engineering giant Balfour Beatty was also dismissed.
The judge made his decision after listening to submissions, reviewing evidence and considering issues which had arisen.
He did not give reasons.
Mr Justice Mackay told jurors: "It is not open to you to convict any of the six defendants on charges of manslaughter. The trial will proceed on the health and safety charges faced by all the defendants.
"I am not permitted to give reasons for the decision. I must ask you to accept my ruling, which does not affect one way or the other the important decisions you will have to make when considering verdicts on the health and safety counts."
Balfour Beatty and the five men - together with Railtrack, which became Network Rail - still face charges brought under the Health and Safety Act.
Four people were killed and 102 injured in the 115mph Hatfield crash on October 17 2000
They were Robert Alcorn, 37, from New Zealand, Steve Arthur, 46, of Pease Pottage, West Sussex, Leslie Gray, 43, of Tuxford, Nottingham, and Peter Monkhouse, 50, of Headingley, Leeds.
The five executives - three from Railtrack and two from the engineering company Balfour Beatty - had denied manslaughter.
They are: Balfour Beatty Rail Maintenance Ltd's regional director Anthony Walker, 46, and civil engineer Nicholas Jeffries, 53, Railtrack London North East zone asset managers Alistair Cook, 50, and Sean Fugill, 50, and Railtrack LNE track engineer Keith Lea, 53.
They also deny Health and Safety Act charges.
Balfour Beatty faced a corporate manslaughter charge and both the company and Network Rail faces health and safety charges, which are all denied.
Prosecutors have alleged the crash was a disaster waiting to happen - but should
have been avoided.
Rail executives had thrown out the rule book when dealing with a large backlog of defects which built up on the line, prosecutor Richard Lissack QC told the jury when opening the case.
He alleged the derailment occurred because:
* A faulty rail at the crash site was identified 21 months before the crash but left unrepaired - although a replacement rail had been delivered and left alongside it for six months;
* Speed restrictions were not imposed in the area of that faulty rail;
* A backlog of essential work had been allowed to accumulate which could have closed down King's Cross station if the rule book had been followed;
* The clock which counted the time for carrying out all of the out-of-date repairs was turned back to zero on the backlog of 200 defects in the first 43 miles of the track from King's Cross.
Mr Lissack said that "this cavalier approach to the safety of those in trains" was finally realised on October 17 2000 - when four people died in coach G as their train left the track travelling at 115 mph.
He alleged Balfour Beatty had been getting "seriously behind in remedying defects on the line".