The Advertising Standards Authority backed the Farmers Union of Wales and one farmer, who complained that the newspaper ad was misleading.
In it, the RSPCA stated that cattle-to-cattle transmission was the main cause of the spread of TB, and not badger-to-cattle.
"So what are some farmers putting pressure on the government to do about it? That's right, slaughter thousands of badgers," the ad read.
The farmers who complained pointed out the spread of bovine tuberculosis was much more complicated than that.
Despite the RSPCA claiming scientists backed its assertions, the ASA noted several reports into cases of bTB, which could not come to a conclusion about how it had been spread.
One recent study found that badgers could have caused anything between 26% and 85% of bovine tuberculosis cases in 2002/3.
"We concluded that the RSPCA had not substantiated the claim or shown that it was generally agreed by informed opinion," the ASA report said.
The charity claims massive public opposition to the proposal to kill thousands of badgers, with 95% of respondents to a public consultation on badger-culling opposed a cull.
The RSPCA believes the government must reject a cull now and concentrate instead on effective ways to combat the spread of TB.
Its campaign is backed by a host of celebrities including the actor Anthony Head, of 'Little Britain' and 'Buffy the Vampire Slayer' fame, Mel C, Joanna Lumley and Jilly Cooper among others.
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