Is qPCR efficiency under 90% acceptable?

To put it bluntly, No!

qPCR efficiency under 90% is not acceptable. The efficiency should be between 90 to 110%. If you are experiencing less than 90% efficiency you may have:

• Poorly designed PCR primers
• PCR inhibitors in your samples
• Inconsistent pipetting techniques leading to inaccurate sample and reagent pipetting