Background
Axis ticks can be converted to scientific format as suggested here.
Numbers can be converted into engineering format, one at a time as shown here
Question
How to format axis ticks in engineering notations i.e. order of magnitude is a multiple of 3.
You may want to explain exactly what you mean by "engineering notation", but there is an EngFormatter, which automatically uses the SI unit prefixes (ie micro, milli, kilo, mega, etc.)
fig, ax = plt.subplots()
ax.set_ylim(0,1e6)
ticker = matplotlib.ticker.EngFormatter(unit='')
ax.yaxis.set_major_formatter(ticker)

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