The Crown had alleged that Mr Ashley breached his duty of care to those who were killed by "exposing them to substantial risk to life when no other lives were at risk".
Mr Woodward was alleged to have breached his duty of care to the four by failing to end the deployment of colleagues wearing breathing apparatus for the purpose of "offensive" firefighting.
Warwickshire's Chief Fire Officer reacted to the not guilty verdicts by condemning the decision to press criminal charges against three members of his brigade.
Graeme Smith is now calling for the Home Office and Ministry of Justice to investigate how and why the prosecution was allowed to proceed.
The fire chief, who was present in court during much of the six-week trial, said: "It is crystal clear that these cases should never have been brought to court in the first place.
"But today neither I nor any of my colleagues in the Warwickshire Fire and Rescue Service feel any sense of relief. Rather we feel a sense of sorrow and remembrance for the four brave firefighters who died at Atherstone-on-Stour in 2007."
Both Warwickshire Fire and Rescue Service and the Chief Fire Officers Association have serious concerns about the case.
Mr Smith and both bodies will be writing to the Home Secretary and to the Justice Secretary to seek a formal investigation into the prosecution.
Voicing concern that such prosecutions may make fire commanders more risk averse, possibly impacting on the safety of the public, Mr Smith was also critical of "undue aggression" shown towards the firefighters charged with manslaughter during their time in police custody.
During two days in the custody of Warwickshire Police, Mr Simmons, Mr Ashley, and Mr Woodward had their belts and shoelaces taken away and were also held at a police station overnight between interviews.
Mr Smith said: "The police investigation into this fire took a wrong turn very early on.
"The police treated decent fire officers like common criminals. The court heard they were locked up in the cells overnight and even had their shoelaces taken away from them.
"It has taken almost five years and five million pounds of public money to construct a flimsy case against these three men and when it was presented in court it simply fell apart."
Police investigations into the death of firefighters had been completed more rapidly elsewhere in the UK, enabling lessons to be learned swiftly, Mr Smith also said.
But the Atherstone-on-Stour inquiry was handled poorly and put firefighters' safety behind the needs of the police inquiry, Mr Smith alleged.
There were two independent reports into the blaze, one commissioned by the police and another commissioned by the Warwickshire Fire Service, which was seized by the police before Warwickshire Fire Service had a chance to consider it.
Mr Smith said: "Both of these reports contained safety critical information of vital importance to the safety of firefighters up and down the country.
"Neither of them was released to the fire service until May 2011 - an incredible three-and-a-half years after the fire.
"I am outraged that the secrecy surrounding these reports meant that firefighters remained at risk for so long."
Addressing the wider issue of whether the fear of prosecution may affect firefighters' decisions as they seek to protect people and property, Mr Smith added: "I am seriously concerned - and the public should be seriously concerned - that today, up and down the country, fire officers will be asking themselves... why on earth would I ever want to be an incident commander and face an unjustified legal attack in the way these three men have
The officer in charge of the £4.6 million inquiry into the Atherstone-on-Stour tragedy conceded that "difficult and unpopular" decisions were taken during the investigation.
Detective Superintendent Ken Lawrence said the scale of the joint inquiry by Warwickshire Police and the Health and Safety Executive was justified by the fact that three men were charged and brought to trial.
Describing the inquiry as one of the most complicated undertaken by Warwickshire Police, Mr Lawrence said: "I think that the investigation has answered a number of important questions, in particular for the families that have lost loved ones.
"I very much hope that the fire service generally will take on board some of the lessons learned from this tragedy and reflect upon them."
The probable cause of the blaze was found to be a naked flame - after all other possibilities were excluded - and Warwickshire Police arrested several people on suspicion of arson.
But although migrants workers at the vegetable packing plant were interviewed through interpreters in around a dozen languages, there was insufficient evidence to charge anyone with arson.
Asked about criticisms of his force's treatment of the defendants who stood trial, Mr Lawrence said he had led a highly professional inquiry in an independent manner.
"Where there is a loss of life, nobody is above investigation," he said. "We must never ever lose sight of the fact that four people lost their lives."
