Piezo pickups sense pressure. If the E strings seems to match in acoustic output, this problem generally means the pickup isn't flush with the saddle slot and/or the bottom of the saddle. It's a common problem on inexpensive guitars with under-saddle pickups.
The other cause is the pickup isn't lined up with the saddle exactly right.
Fixing it is a protracted trial-and-error process. Make sure the bottom of the saddle is dead flat. Precision machining is the best way, but using a thick pane of glass as a base to sand the saddle works. Ensuring the slot is also flat is a guitar tech problem. Find one who knows and has experience with piezo under-saddle PUPs.
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