Hope someone can help, have yet to find a solution to this problem....
My 2002 Rx300 was in the shop having some body work done, to my understanding the battery died at some point while it was there and had to be charged back up but ever since the alarm won't stop going off. The guy at the shop said he had obtained the "code" from Lexus and "fixed it" but he really just cut the wire to the alarm speakers so now there's an annoying clicking noise that can be heard inside the car and the lights flash when the alarm goes off but no other sounds. The alarm is triggered any time I open or close the car either with the remote or with key and when I'm driving I can hear the clicking sound of the alarm every few minutes. I've tried disconnecting the battery for 30 minutes and that didn't work, turned the key left then held right for 3 seconds, unlocked the car with key followed by remote then turned it to "on" and let it sit for 30 seconds.... Other ideas?

 

Turn the key in the passenger door, it should reset the alarm system. If that doesn't work try the rear lift gate with the key. I forget which door it is so just try both. If the problem still doesn't go away check the battery in the remote. Some cars have the alarm go off, when the battery in the remote is low.

 

So I was really excited to find this post, only to realize that it's my own post from 2010. Yay. Same body shop, same problem. Battery was changed, I only have 1 master key and the alarm wires have been disconnected again. The clicking of the alarm every few minutes is maddening and I wasn't able to get it fixed last time. Had to pay Lexus a good amount of $$ to fix my problem but now that my battery died again I'm back at step 1. I've tried Programming the Remote Entry "Make sure no key in ignition, driver door open and another 3 doors are closed and locked.
Insert the master key into ignition switch then remove it. Lock and unlock driver door 5 times( use the lock and unlock buttom at the door handle, not the master switch).
Then close and open the driver door one time.
Lock and unlock driver door 5 more times (at the door handle, same like the second step).
Then insert the master key in ignition and turn it on and then off. Remove the key. You hear the door lock and unlock itself once.
Then press the lock and unlock bottoms on the key (at the same time) and hold it for about 3 seconds.
Release both bottoms and then just press the unlock bottom for about 3 seconds and you should be done with reprogramming the remote entry."
but no luck.... Passenger door and rear lift gate solution don't work either.... Any other tricks?

 

How many keys in total? Just the one master you mentioned?

 

Yes, just the 1 key...

 

Oh, ok. Nevermind then.

The procedure I was going to list for resetting the security system a different way requires more than one key.
-Unhook the battery, reconnect and then you literally take each key you have and stick it in the ignition for a few seconds each.