A detailed complaint had been made to the Commission by the National Farmers' Union (NFU), who said the RSPCA and its chief executive, Gavin Grant, had "overstepped the mark". It raised concerns about the RSPCA's campaign, including Mr Grant calling for farmers involved in the badger cull to be named, and for a boycott of milk from farmers in badger-cull areas.
The Charity Commission said yesterday: "We have now closed our case and have concluded there are no outstanding regulatory concerns".
However spokeswoman Tallulah Perez-Sphar later added: "We expect to meet the trustees soon in order to discuss the wider issues raised by this case and by the RSPCA's activities in general."
NFU President Peter Kendall said: "We had very real fears that any farmers named, as called for by the chief executive of the RSPCA, would be threatened, intimidated and harassed by others.
"Farmers have always understood the RSPCA to be a charity that works to safeguard the welfare of animals and we have no issues with its charitable work.
"As a charity, the RSPCA has a privileged status, but it must respect the law that applies to charities.
"I am extremely grateful to the Charity Commission, who took our complaint seriously and carried out a thorough investigation of the issues we raised. The RSPCA has now clarified its position on the naming of farmers involved with the badger cull – and that it condemns personal intimidation. The RSPCA has also now confirmed that it will not call for a boycott of milk."
In a statement, the RSPCA said neither Mr Grant nor the RSPCA had at any time threatened to name and shame anyone taking part in the badger cull.
"The RSPCA condemns all harassment, intimidation and violence," it stated.
However last November, speaking on the BBC Panorama programme, Mr Grant said: "The spotlight of attention will be turned on those marksmen, and on those who give permission for this cull to take place. They will be named and we shall decide as citizens of this country whether they will be shamed."
Six-week pilot culls of badgers, using marksmen with rifles at night, are currently taking place in West Somerset and Gloucestershire as part of the Government's campaign to eradicate bovine tuberculosis, responsible for the death of 28,000 cattle last year. Animal rights protesters are trying to disrupt the shooting.