I had this issue on my hybrid.
It turned out simply to be the 12v battery. the one that also lives in the boot passenger side.
It turns out that the 12v battery supplies the electricity to the hybrid electronics and my theory is as follows.
The 12v battery held enough voltage and everything was working fine so at first I did not suspect it as the cause.
I removed it and charged it at home and when I put it back in the car everything was fine. The "check hybrid system" and the CEL light turned off.
I noticed that the cells in the 12v battery had allot of sulphation so I suspect that the internal resistance of this battery is quite high.
And the lexus is not happy and not able to charge this battery adequately.
I have since replaced the battery and everything still remains fine.