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This question was helpfully answered on Github by jcopperfield, here is the solution;
// centre x-scale label
var xScale = myBubbleChart.scales['x-axis-0'];
var xLabelOffset = (xScale.getPixelForTick(1) - xScale.getPixelForTick(0)) / 2;
myBubbleChart.options.scales.xAxes[0].ticks.minor.labelOffset = xLabelOffset;
// centre y-scale label
var yScale = myBubbleChart.scales['y-axis-0'];
var yLabelOffset = (yScale.getPixelForTick(0) - yScale.getPixelForTick(1)) / 2;
myBubbleChart.options.scales.yAxes[0].ticks.minor.labelOffset = yLabelOffset;
// update chart
myBubbleChart.update();
Source:stackexchange.com