The RSPCA has apologised to the Farmers Union of Wales for the charity’s "adversarial and highly politicised campaigns".
The union still says many questions remain regarding the organisation’s conduct and that of the Charity Commission, which is responsible for monitoring charities.
Jeremy Cooper, the new Chief of the RSPCA told The Telegraph: "Of course we have made mistakes in the past, and we are very sorry about that.
"We have to be honest and admit the mistakes and acknowledge them."
The apology comes after years of criticism and negative publicity which led to a parliamentary inquiry and an independent report recommending sweeping changes to the charity’s involvement with prosecutions.
Responding to the apology, FUW Deputy President Brian Thomas said: "For more than a decade the FUW repeatedly raised concerns about the conduct of the RSPCA in relation to its overtly political campaigns.
"We pursued a number of complaints with the Advertising Standards Authority and the Charity Commission, amongst others."
Mr Thomas said that while the ASA had upheld complaints against the RSPCA by the FUW, the Charity Commission had, over a prolonged period, appeared to take a passive approach to the charity.
"In response to serious complaints against the RSPCA the Charity Commission was generally dismissive and at times appeared to try and brush concerns under the carpet.
"Their passive approach to the RSPCA effectively gave the charity a green light to become more militant and more political, and we would argue that Mr Cooper’s public apology is at least in part a direct consequence of this failure by the Charity Commission," added Mr Thomas.
'The oldest law enforcement agency'
In 2012, the then Chief Executive of the RSPCA, Gavin Grant, described the charity as "the oldest law enforcement agency still in existence in this country", and threatened to campaign to "stop consumers drinking milk", if supermarkets were unable to differentiate between "badger friendly milk" and milk from English badger cull areas.
Similar, more ominous threats were made during a 2012 BBC Panorama documentary on the English badger cull, during which Mr Grant said that: "The spotlight of attention will be turned on those marksmen [employed to cull badgers] and on those who give permission for this cull to take place.
"They will be named and we will decide as citizens of this country whether they will be shamed."
In 2012, the FUW wrote to the President of the Association of Chief Police Officers expressing major concerns that ten police forces in the UK, including the North Wales and South Wales Forces, had agreements with the RSPCA which allowed the charity to access confidential and sensitive information about individuals contained in police records.
Concerns have also been expressed after the RSPCA tried to claim thousands of pounds for stabling and caring for horses which had been put down by the charity.
"A sinister shadow has been cast over the honourable roots of the RSPCA and the important work done by its employees.
"The only way in which to redeem its reputation is through full transparency, and a full investigation of the role played by the Charity Commission in allowing the organisation to fall into such disrepute," said Mr Thomas.
'We accept our tone on some campaigns may have been wrong'
The RSPCA said: "Our position on hunting, the badger cull and campaigns remains exactly the same but we accept our tone on some campaigns previously may have been wrong.
"The RSPCA remains as committed as ever to speaking out for vulnerable animals.
"We make no apologies for our campaigning work which has resulted in the introduction and amendment of many laws to protect our pets, wildlife, farm animals and animals used in research, but we accept we got the tone wrong sometimes.
"Likewise, we make no apologies for prosecuting people in instances where there is clear evidence of animal cruelty.
"We do however apologise for the specific incidents where we have got it wrong.
"We apologise for past mistakes where an investigation wasn’t carried out to the standard we would hope, both for the animal involved and their owners.
"The RSPCA is not a political organisation and has no affiliation to any political party.
"We do, however, do everything we can to improve animal welfare and often the only way to do this is through changes to the law.
"We work with our supporters, MPs and ministers, regardless of who the government is at the time.
"The RSPCA will continue to speak out on matters where we believe animal welfare is compromised or could be improved. That does not make the RSPCA a political organisation.
"Our campaigns are carried out in accordance with charity law and the Charity Commission’s published guidelines which recognise that campaigning and political activity can be legitimate and valuable activities for charities to undertake.
