The former president of Ivory Coast is to be released and charges of crimes against humanity dropped after the international criminal court ruled he had no case to answer.

The court in The Hague acquitted Laurent Gbagbo and his former youth minister of all charges and ordered their immediate release.

The charges, which included ordering murder and gang-rape, related to post-election violence in the west African country in 2011. Gbagbo refused to hand over power to Alassane Ouattara, the current president, and about 3,000 people died in the aftermath. After French troops and the UN intervened, Gbagbo was prised out of the bunker where he was hiding with his wife, Simone.

The judges ruled that Gbagbo and his then youth minister, Charles Blé Goudé, had no plan to keep Gbagbo in power, and so there was “no need for defence to submit further defence, as the prosecutor has not satisfied the burden of proof”.

The decision will be a severe blow for the ICC prosecutor, for whom it was a landmark case. The court will resume on Wednesday, where the prosecution will say whether it intends to appeal, and if it does, what conditions it wants to impose on Gbagbo’s release.

The ICC has been accused of being one-sided as it did not bring any charges against pro-Ouattara commanders who were also accused of abuses. Ouattara, who was re-elected in 2015, has been accused by his opponents of using the ICC to silence opposition.

There has been little justice for the victims of the post-electoral violence: although Ivorian judges investigated many of the crimes and charged military and political officials from both sides, last year Ouattara announced a controversial amnesty for 800 implicated people.

The ICC’s chief prosecutor, Fatou Bensouda, confirmed that the investigations in the Ivory Coast would continue, including, presumably, the massacre at Duékoué of March 2011, in which at least 800 people died.

She said: “My office is vigorously dedicated to doing its part, with the plight of the victims in Côte d’Ivoire foremost and always on our minds.”

Human rights organisations said the acquittal was “disastrous” for the victims.

“While the acquittal of Laurent Gbagbo and Charles Blé Goudé shows that the rights of the defence are respected at the ICC, it is at the same time disastrous news for the victims who are left with no possible remedy,” said Pierre Adjoumani Kouamé, the president of the Ivorian Human Rights League.

Drissa Traoré of the International Federation of Human Rights said the court ruling could lead to further violence.

“Between the amnesty decree issued by President Ouattara and the acquittal of Laurent Gbagbo and Blé Goudé at the ICC, there is a risk of wholesale impunity for the 2010-11 crimes. The Ivorian government and the international community are leaving 3,000 victims and their families with no recourse to justice,” he said.

“Eight years after the tragic crisis experienced by our country, those same actors risk fuelling the antagonism of the past and the political violence which ensued.”

A former university professor turned activist, Gbagbo spent much of the 1980s in exile in France. After returning, he lost the 1990 presidential vote and spent six months in prison in 1992 for his role in student protests.

He came to power in 2000 in a flawed vote that he himself described as “calamitous”, but he then put off holding another election for a decade. In the 2010 race, Gbagbo came top in the first round with 38% of the vote before losing to Ouattara in the runoff.

The 17-year-old ICC has long been criticised for disproportionately going after Africans. The current prosecutor, Fatou Bensouda, a Gambian, has worked to change that, opening investigations in Afghanistan, Iraq, Palestine and the Ukraine.

The Gbagbo decision was “yet another major blow” for the ICC prosecution, which has yet to show that it is up to the task of sustaining charges against powerful people accused of the most serious crimes, said James Goldston, the director of the Open Society Justice Initiative.

“The acquittal underscores how important it is that the process to select the next prosecutor yields a person of integrity and sound judgment who is highly skilled at criminal investigation,” he said.