Citizens Advice Scotland (CAS) said its service saw more than 46,500 instances of unfair treatment at work last year.
This was an increase of 5.5% on the previous year.
It cited examples of unfair dismissal, non-payment of wages, cancellation of holidays, bullying and racism.
CAS said it had been told by many workers that they would like to take their case to tribunals but could not afford to do so.
Its report, called Fair Enough?, sets out issues in detail and suggests solutions "to make Scotland's workplaces fairer".
Recommendations include removing Employment Tribunal fees, and creating a new statutory Employment Commission to oversee the enforcement of employment law and promote fair employment.
•Employees who were not paid at all by their employers - in one case for six months' full-time work
•Clients who were unfairly denied sick pay when seriously ill
•Employers refusing to allow employees to take paid holiday
•Women who were dismissed when they became pregnant
•Migrant workers who were exploited and made to work excessive hours
•Clients who could not afford the fees for an Employment Tribunal claim
The report is being sent to government ministers, MPs and MSPs.
It is part of a wider CAS campaign which aims to highlight unfair employment practices and remind workers of their rights.
CAS spokesman Rob Gowans said: "We know that many Scots who are unemployed face severe hardship. But many who do have jobs are living on low incomes and also facing extremely unfair conditions at work.
"The evidence we present today is a snapshot of the kind of employment cases we see.
"Of course it's important to say that most employers are fair and treat their staff well.
"But sadly it's clear that there are many rogue employers in Scotland, and also that the system is in many ways stacked against workers who want to challenge unfairness at work."
He added: "Some of the unfair employment practices we see put workers in difficult, complex and miserable situations.
"In exposing these today we want to raise awareness of these problems, but also to argue the case for change."
A Scottish government spokesman said: "Employment law is reserved to the UK government.
"While the vast majority of employers in Scotland are lawful and exercise a duty of care to their employees, there are unfortunately people who flout the law.
"The Scottish government fully recognises the importance of making workplaces fairer.
"We have announced our intention to set up a Fair Work Convention to encourage government, employers, trade unions and employees to work together to establish progressive workplace practices, boost innovation and productivity.
"We are also considering the implications of the new powers around tribunals that are being transferred as part of the Smith process."
Thousands of Scots face unfair working practices which leave them in "desperate and miserable situations", according to a report.