A regional council spokeswoman said chief executive Andrew Newman would not be commenting further than the statement released on Monday.
HBRC chairman Rex Graham said he thought the decision to withdraw the prosecution was "very sensible", as it meant the councils would now be able to work better together.
The announcement came hours after a hearing of the Government inquiry about ensuring the safety of Havelock North's drinking water, which the prosecution was accused of derailing.
Mr Yule said the district council had requested the prosecution be withdrawn two weeks ago, but the agreement was not reached until Monday night.
When asked if he thought the hearing had something to do with this, Mr Yule said he could not comment.
"But clearly the regional council were prepared to accept the request we made of them a couple of weeks ago after a day in court, so one has to draw their own conclusion about that."
The panel had no comment to make on the prosecution, directing Hawke's Bay Today to comments made by inquiry chairman Justice Lyn Stevens QC during the hearing.
On Monday, he quizzed both HBRC resource management group manager Iain Maxwell, and Mr Newman about the prosecution: Why charges had been laid at the start of the inquiry, and whether the prosecution could be withdrawn.
He also berated them about the prosecution resulting in a delay of the inquiry, and consequently, a delay in finding the cause of the contamination.
As of November 14 the investigation had cost $440,700, with around 2360 staff hours spent on it.
Mr Graham said the investigation had been a very expensive process, which neither council had budgeted for.
Earlier this year the regional council was told some of the costs related to the investigation could be recouped if there was a successful prosecution. At that time, Mr Maxwell said this could come through penalties imposed on one or a number of parties if a prosecution was undertaken.
When asked yesterday if the HBRC would look to recoup the costs elsewhere, he said it had sufficient reserves available to cover the costs, and this expenditure would not affect any future spending.
When asked how staff were feeling now about the prosecution being withdrawn, Mr Maxwell said they were "passionately committed" to understanding what happened in the contamination, and would continue to work hard to assist the inquiry.
"All the information gathered by HBRC will be fed into the inquiry to help understand what happened in the Havelock North drinking water contamination," he said.
Mr Yule was not sure how much time, or money had been spent by the district council relating to the prosecution.
"We were preparing for today's inquiry and after that we would have gone on to the prosecution, so I don't believe a great deal of work has been done," he said.
"I do know that the costs of the prosecution in defending our position will largely be met by our council's insurance policy."
