A Slovakian court has acquitted a well-connected businessman of ordering the murder of an investigative journalist in a case that exposed high-level political corruption, ultimately toppling the governing party.

The judges said there was not enough evidence for the conviction of Marián Kočner and a co-defendant over the killings of Ján Kuciak and his fiancee Martina Kušnírová, both 27.

A third defendant was convicted and sentenced to 25 years in prison. Prosecutors can appeal against the acquittals.

“The crime was committed but it has not been proved that ‎Marián Kočner and Alena Zsuzsová ordered the murder,” the judge Ružena Sabová said in her ruling.

Kočner received a €5,000 fine for illegal weapons possession, relating to 60 bullets found in his house.

Kuciak’s father, Jozef, said he was “left paralysed” by the verdict. “We can only hope that justice will eventually prevail,” he said.

The killings prompted street protests unseen since the 1989 anti-communist Velvet Revolution and a political crisis that led to the collapse of the government.

Slovakia’s prime minister, Igor Matovič, elected on the back of the wave of protests in the wake of the murders, said it was “obvious masterminds behind the murder want to get out of the clutches of justice”. “We believe that justice will wait for both of them,” he said in a post on his official Facebook page.

The president, Zuzana Čaputová, also elected on the back of the outrage, said she was shocked by the verdict and she expected it to be appealed in the supreme court.

Kuciak was shot in the chest and Kušnírová was shot in the head at their home in the town of Veľká Mača, east of Bratislava, on 21 February 2018. Prosecutors told the court that Kočner, who had ties to senior politicians, had allegedly threatened the journalist following the publication of a story about his property dealings.

They argued that Kočner ordered Kuciak’s murder in revenge for his articles, and called for the businessman and two alleged accomplices, Zsuzsová and Tomáš Szabó, to be jailed for 25 years if convicted.

Two other defendants were previously convicted and sentenced. Miroslav Marček, a former soldier, pleaded guilty to shooting Kuciak and Kušnírová and was sentenced to 23 years in prison in April. Prosecutors alleged Kočner paid Marček to carry out the killings.

Another defendant, Zoltán Andruskó, agreed to cooperate with prosecutors in exchange for a lesser sentence, and received a 15-year prison term in December. He testified that Kočner ordered the murders.

Prosecutors argued that Andruskó served as a go-between, hiring the gunmen Marček and his cousin Szabó at the request of his friend Zsuzsová, who in turn was following Kočner’s orders.

Kočner denied murder in his closing speech in the trial in July. “I am not a saint but I am not a murderer either. I’m certainly not a fool who wouldn’t realise what a journalist’s murder would lead to,” he told the jury.

In June he addressed Kuciak’s father in court, saying: “I’m sorry about what happened to your son, believe me, but I have nothing to do with it.”