The target, set by the SNP in its 2018 programme for government, was due to be hit by the deadline of September 2020, but a freedom of information request by the Liberal Democrats shows just 215.35 counsellors had been allocated to secondary schools.
Scottish Government officials disputed the claim, stating they were confident the target had been met due to the 350 figure based on the number of secondary schools in the country and many local authorities deciding to use a area-wide approach rather than a school-by-school approach.
They added that all secondary schools in Scotland “have access” to counselling services.
Liberal Democrat MSP Beatrice Wishart called on the Scottish Government to ensure pupils had quick access to counselling as the pressure of the 2021 exam season ramps up.
She said that with children sitting assessments “thick and fast”, the potential damage of a delay to support could have “serious implications”.
She said: “It's a particularly stressful few weeks for pupils, at the end of a turbulent year. Young people are in the middle of exams they were told were cancelled.
"The documents published online as a result of our investigation show only 215 of the 350 counsellors promised by the Scottish Government in 2018 actually attached to schools.”
The party added that when it had asked the Scottish Government for details on the number of counsellors hired, the figures were “withheld” by education secretary John Swinney prior to the election.
Ms Wishart added: “The Scottish Government says the target has been "reframed". However, it is far from clear how many more full-time counselling staff are actually available to pupils through other routes. Parliament was given the run-around in its efforts to get to the bottom of this.
"Assessments are coming thick and fast. The slightest delay to accessing support could have serious implications. After heaping so much on pupils', SNP ministers need to demonstrate that there is consistent and quick access to support. Young people deserve that reassurance.
"The routes to support must be more visible than ever. The full complement of counsellors need to be there for young people or, better still, even more staff could be added to help with the serious situation which is emerging."
In the 2018 programme for government, the SNP committed to an investment of £60m in additional school counselling services, adding that it would ensure “every secondary school” has access to counselling services for pupils across the country.
Responding to the Liberal Democrat claims, a spokesperson for the Scottish Government said: “The mental health and wellbeing of children and young people is an absolute priority for the Scottish Government.
“The approximate figure of 350 counsellors is the commitment related to the number of secondary schools in Scotland. We are confident we have met the commitment in full and that all secondary schools in Scotland now have access to counselling services.”