The wider British figures show that renewable capacity in England was higher than in Scotland for the first time.
The change was explained by "considerable" use of bioenergy south of the border, amounting to 91% of the UK total. Much of that growth is because of the conversion of Tilbury B power station, Essex, in 2011.
Hydro accounted for 39% of renewables generation in Scotland but because bioenergy is more intensive, generation from renewable sources in England was 27% higher than generation in Scotland, the statistics show.
Renewable capacity in Scotland increased in each quarter from 4,451 MW at the start of 2011 to 5,453 MW in the second half of 2012.
Conservative MSP Murdo Fraser, convener of the Scottish Parliament's Energy Committee, said: "The whole problem with the Scottish Government's approach to renewable energy is that it's focused almost exclusively on developing more wind farms. Wind power is an unreliable and intermittent form of energy production."