Details obtained by the Scottish Conservatives using a parliamentary question show just 63.5 per cent of cases were resolved within the set time frame.
The Tories said the figure, which has fallen from 74 per cent in September 2013, showed court closures were “beginning to bite”.
But the Scottish Courts and Tribunals Service (SCTS) said fewer cases were being dealt with within the 26-week period due to a greater focus on more complex cases involving domestic abuse and historical sexual offences.
Douglas Ross, the Scottish Conservative’s justice spokesman, said: “When the Scottish Government embarked on this unnecessary and unpopular round of court closures, it was warned of the impact.
“Now we’re seeing exactly that, with a third of cases taking longer than the 26-week target time frame to conclude.
“That’s not good enough for the victims of crime, and it’s clearly left the remaining courts with an increasing backlog.”
He added: “This was an ill-judged decision by the SNP.”
Ten sheriff courts and seven justice of the peace courts were closed after the proposals were accepted by the Scottish Government and backed by MSPs in 2013.
The new figures also showed that the length of time taken to reach a verdict from an initial charge has increased.
But the SCTS said its own target of offering trial dates within 16 weeks of cases first calling in court was being met in 97 per cent of cases, up from 50 per cent in 2014.
A spokesman said: “The increased complexity and numbers of cases proceeding to evidence-led trials has no connection at all with court closures.
“Cases that transferred from closed courts amounted to only five per cent of overall court business.
“In 70 per cent of courts receiving transferred cases, the courts performance against the Scottish Government 26 weeks target has improved since the court closures.”
A Scottish Government spokeswoman said: “There is no evidence to suggest that court closures has had any impact on the time it takes for cases to go through the courts.
“The rise of reporting and prosecution of certain types of crime has put extra pressure on the courts.
“We have already allocated nearly £1.5 million for extra fiscals, judiciary and administration staff to help respond to delays and speed up access to justice for victims and witnesses, and are spending an extra £5 million improving efficiency of cases involving domestic abuse and sexual offences.”