Emissions rose slightly (0.8%) in 2012, bucking a general downward trend over the last decade.
In 2012, emissions were estimated to be 55.6 million tonnes carbon dioxide equivalent (MtCO2e), above the target of 53.226 Mt.
Environment Minister Paul Wheelhouse said that achieving the Scottish Government's "ambitious" targets "is in fact even harder than Parliament and society realised".
Environmental groups criticised the missed target but described the Government's action to tackle emissions as "promising".
Labour said the missed target is "deeply embarrassing" for the Government, while the Greens called for "bolder action" to reduce emissions.
Mr Wheelhouse said: "Scotland chose to have stretching targets because we were aware of the scale of the challenge of climate change. And we should be proud of the efforts that have been made across society since the 2009 Climate Change Act.
"However since then we have also improved the method for calculating our greenhouse gas emissions. That was the right thing to do, but it now shows that the task is in fact even harder than Parliament and society realised in 2009.
"The Scottish Government has therefore put together a package of measures to demonstrate our resolve to meet future targets and ensure Scotland remains a world leader in this field."
Gina Hanrahan, from Stop Climate Chaos Scotland, said: "It's been a difficult start to the implementation of the Climate Change Act, but the Scottish Government's package of new measures across different sectors such as energy efficiency, low-carbon travel and district heating looks promising.
"We look forward to further details being announced later today, but so far this looks like a sign of serious intent."
Ian Marchant, chair of Scotland's 2020 Climate Group, called on "all sectors of Scottish society to reinvigorate efforts to meet the targets".
He added: "Scotland should be leading the way and demonstrating its credentials and this is only possible if people realise it's not going away - climate change is not a scientific myth, and measures to reduce should be a vital component of any successful business.
"If we are serious about tackling carbon emissions and the future of our children and grandchildren, we have to have reliable and up-to-date data to be able to assess the impact of policies and changes - having 2012 data released in 2014 isn't helping us."
Labour environment spokeswoman Claire Baker said the missed target "is deeply embarrassing for a Scottish Government that continually heralds them as world leading".
She added: "The minister must now fully explain why, under his watch, emissions have risen in the past year and the SNP Government have failed to make the step-change needed."
Green MSP Patrick Harvie said: "This latest failed target will strengthen the growing mood in support of bolder action from Government, and it's essential that the climate change minister takes the opportunity to act.
"There's agreement across the parties at Holyrood for a series of additional policies to cut our greenhouse gas emissions, and it's simply not good enough for ministers to wheel out the same old rhetoric.
"This afternoon's statement must give detailed plans to get Scotland back on track. Re-announcement of existing commitments would be simply unacceptable."