Instead, Mr Whittall and Pike River Coal have offered a voluntary payment on behalf of the directors and officers of the company to the families of the men and two survivors, in what has been described as "blood money" by one widow.
However, Judge Jane Farish said the surprise turn of events was not a case of a chief executive "buying his way out of a prosecution".
She told the Christchurch District Court this morning the likelihood of a prosecution was "extremely low" and the case may never have reached trial. The decision not to prosecute was taken at "a very high level", she said.
"Some people may believe this is Mr Whittall buying his way out of a prosecution. But I can tell you it's not," Judge Farish said.
She said the reparation was a "side issue", and described the case's conclusions as a "good outcome".
The compensation was an acknowledgement the company failed the 29 men who died, and on that basis she was prepared to discharged Mr Whittall of all 12 charges.
In a statement from four former heads of Pike River Coal, including Mr Whittall, they said the money that would have been spent defending the case would now go to the families.
It means $110,000 will be given to each of the families and survivors - totalling $3.41m. The directors have also offered to meet with the families.
But the decision has been met with shock by those close to tragedy.
Anna Osborne, who lost husband Milton, said she had lost faith in justice.
"I am sick to the stomach. There is no justice or accountability for the Pike 29," she said.
"It is just another slap in the face for the families. It was not an accident, our men were killed."
The payout was no consolation for her, she said.
"As far as I'm concerned it's blood money."
Melissa Byrne, whose partner, Sam Mackie, 26, was killed in the blast, said the decision was "just another huge kick in the guts".
" I feel that no one's going to be held responsible. Aren't our men worth more than what they're being portrayed to be worth right now.
"A big part of me is not surprised at all but that doesn't take the pain and hurt away. It still feels absolutely devastating."
She said Mr Whittall's prosecution could have been "a start" in the families getting some closure.
"I don't know if there's ever going to be closure for us. It just hurts, it really does hurt."
Bernie Monk, spokesman for most of the families, said "justice just was not served today".
"It's put New Zealand justice back a long way," he said.
"We've always said that this disaster made a laughing stock of mining, and now the justice system is in the same place."
He vowed that the families "won't let this lie".
"We're going to take this further. There's still a conviction that can be done here. The families are going to drive to get down into the mine - not only down into the mine to get the men out, [but] to get the evidence.
"What really frustrates me is that some of those mining guys who worked with our men under ground wouldn't come back to testify. And it's just gutwrenching to hear that today."
Mr Monk said he would "never" meet with Peter Whittall.
"He walked away from us ... and now he expects us to come running to him when he snaps his fingers? That's not going to happen for Bernie Monk."
Carol Rose, whose son Stuart Mudge died in the mine, said it was never been about money for the families.
"And so this feels like blood money - this feels like a back-room deal. There's no justice here.
"There was talk last night about families refusing the reparation. Obviously there was only a small group of us there [in court today], so we can't make that call on behalf of other families, but that's how we feel.
"It's about justice. It's about 29 men going to their workplace and never coming home - they were killed - they didn't die, it wasn't an accident, they were killed, and no one is being held accountable.
"So as Bernie said, it's really important that we get into the mine, we get the evidence, and we bring criminal charges against the person, people, entities, that are responsible for this."
She also said she wouldn't meet Mr Whittall.
Grey District Mayor Tony Kokshoorn said the decision would come as "a massive surprise" to many people on the West Coast.
"There has to be some accountability somewhere and that will be seen as West Coasters as that not being fulfilled.
"Peter Whittall is obviously innocent until proven guilty but there is a system in place and he was charged and unless the reasons for the charges being dropped are absolutely water-tight, West Coasters are going to be very suspicious I think."
West Coast-based Green MP Kevin Hague said it was "absolutely outrageous" that Mr Whittall would not face charges.
"I believe it's an appalling insult to the families of the dead men and their memory that effectively the Government is enabling Whittall to avoid that accountability and justice.
Ged O'Connell, EPMU assistant national secretary, said he was "stunned into silence" when he heard the decision.
"It defies belief that no one can be held accountable - 29 people can die and nobody's accountable," he said.
"It's an appalling indictment on the health and safety culture of New Zealand."
In court this morning the Crown said that after an extensive review it was "not appropriate to continue with the prosecution against Mr Whittall".
The Ministry for Business, Innovation and Employment (BMIE) said after reviewing the case it did not believe there was enough evidence to secure a conviction, and the public interest in the case was "not met by continuing with a long costly trial with a low probability of success".
"Taking into account the available evidence, the ministry considered that the likelihood of obtaining a conviction was low," said acting deputy chief executive of the health and safety group, Geoffrey Podger.
Mark Zarifeh, counsel for MBIE said one of the major problems was "witness availability".
Of the 92 witnesses who had given a brief of evidence, 31 of them had not been signed "for one reason or another".
Of those, 14 witnesses are outside New Zealand - living predominantly in Australia - and the Crown lawyers had to powers to summons witnesses living overseas.
There was also problems over expert witnesses, with both sides holding competing views.
In regards to the $3.41m reparation payment, Mr Zarifeh said the money was "not simply a payment made to avoid continued prosecution".
That statement brought groans, and cries of "yeah right" from family members in the public gallery in court today.
The main reasons given for not continuing with the prosecution were:
* The penalties for the charges against Mr Whittall are fine only.
* The principal offender PRCL (Pike River Coal Limited) has been convicted and fined with record fines and a very substantial order for reparation imposed.
* Mr Whittall is charged as a secondary party on the basis that he acquiesced or participated in PRCL offending.
* The Royal Commission into the Pike River mine disaster has heard extensive evidence and provided a comprehensive report on the causes of the explosion at the mine, the cause of loss of life, and the requirements of the Act or Regulations or other laws governing underground coalmining etc.
* The $3.41m reparation order.
* A prosecution requiring a 16-20 week trial in Wellington will be a "very high cost one in both financial and resource terms and best use of limited resources is an appropriate consideration".
- Additional reporting Patrice Dougan, Matthew Theunissen and Greymouth Star
