Javier Valdez, who was also the founder of the Riodoce weekly newspaper and worked for the La Jornada daily, was shot dead three years ago in Culiacan.
"The negligence of the authorities and the delays in the process make you worry that once again those responsible for the crime will have impunity," said the France-based RSF in a statement.
"Although there has been some progress, justice is being served drop by drop."
On February 27, Heriberto Picos Barraza was sentenced to 14 and a half years in prison after confessing to his role in the murder, but RSF said Valdez's family were denied their "legitimate right" to question him.
According to prosecutors, Picos Barrazza drove the car for Juan Francisco Picos Berrueta and Luis Idelfonso Sanchez, who shot Valdez dead before fleeing.
In the trial it was revealed that the trio had links to notorious Mexican drug kingpin Joaquin "Chapo" Guzman, who is serving life behind bars in the United States.
RSF hit out at the delay in bringing Picos Berrueta, known as "el Quillo," to trial. He is currently being held in pre-trial detention.
"The progress in the search for justice is not what we, as family, would want," said Valdez's wife Griselda Triana.
"They got rid of him because someone didn't like what he wrote. It was that easy," she added.
Valdez, 50, who freelanced for AFP for a decade, was known for writing articles critical of powerful criminal gangs such as the notorious Sinaloa drug cartel led by Guzman.
One of his final pieces was about the internal struggles within the Sinaloa cartel following Guzman's capture in January 2016, before the drug lord was extradited to the US.
RSF regularly ranks Mexico alongside war-torn Syria and Afghanistan as the world's most dangerous countries for news media. Violence linked to drug trafficking and political corruption is rampant, and many murders go unpunished.
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