This is the eighth time in 12 years that the legally binding target has been missed.
Although total emissions in 2021 were 49.9% lower than in 1990, the target for the year was a 51.1% reduction.
The Scottish Government expressed disappointment but noted that it was “not far behind” where it should be.
The government data shows that in 2021, Scottish source emissions of the seven greenhouse gases were estimated to be 41.6 million tonnes carbon dioxide equivalent (MtCO2e), which is 2.4% higher than the 2020 figure.
The main contributors to this increase were domestic transport and residential sectors.
The report suggests there were emissions reductions in the energy, business and international aviation and shipping sectors.
Morag Watson, Director of Policy at Scottish Renewables, said: “Today’s announcement is another wake-up call for the Scottish Government.
“We are in a climate emergency but the pace of decision making and action is falling short of what is needed. Time is running out for the government to put in place a proper plan for how we accelerate our nation’s ambitions for transitioning to net zero.
“The renewable energy industry is already meeting most of Scotland’s electricity demand and we know we can do so much more to help reduce emissions.
“We are ready to work with the Scottish Government to ensure that the right conditions are put in place now in order to deliver a cleaner, greener nation.”