Keith Higginbottom, 39, former editor of the Angling Times , denied two charges under the Countryside and Wildlife 1981 Act that his edition of 4 December 1996 would encourage the killing of cormorants.
After the hearing at Peterborough, the paper's current editor John Kelly criticised the decision to press charges. He also vowed to continue the campaign to take cormorants off the protected list. The birds have been driven inland to feed, incurring the wrath of anglers and fish farmers.
Mr Kelly said the prosecution was an "absolute waste of money".
"The decision to bring [the case] at all has to be questioned as it was a serious challenge to journalistic independence and free speech which is the hallmark of a democratic and free country."
The edition which led to the charges being brought carried the headline "These birds must be killed" opposite a picture of a masked, armed man - and four dead cormorants. The prosecution alleged that it contained 13 specific messages about the need to kill cormorants.
Kevin Saunders, of the League Against Cruel Sports, said: "When we saw the article we were very worried about it and we were certain it was a clear incitement to people to kill a protected species. The outcome is very disappointing and we just hope people are more responsible in the future."
An RSPCA spokeswoman added: "These birds are protected and even if someone believes they are causing a problem, it is not up to any individual to decide what should be done.Reuse content