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I have a 2005 Sienne XLE with 31,000 miles on it.  Recently the A/C stopped working.  I brought it into a dealer and was told it needed a new magnetic clutch, that it was under warranty, but that the part was on national backorder.  After being without A/C for a couple weeks (in NC it is tough during summer months), the dealer insisted they called all over and couldn't find one.  I ended up finding one myself in San Diego, had it shipped overnight, and had it put on.  It cost me $650!  They tell me my warranty expired as of 10/3/2007 because the car was "put in service" when the dealer got in...I bought it from the dealer with 4,000 miles on it...now an told I am outside the warranty.  3 years or 36,000 miles...3 years came first and Toyota refuses to honor fixing it.  The issue is that there were NO magnetic clutch units available anywhere and they have been on national backorder now for almost a month.  Sounds like there is a problem that Toyota is not fessing up to.  I had hoped they would be different from other car companies and dealers, but alas not.  I just traded my Lexus in on an American car and will probably do the same with the van shortly.  They lost a customer because of poor service and not doing what is right.  

I, too, have a Toyota [2002  XLE V-6] A/C malfunction.  I was hearing a 'bearing' type of rattling but the A/C was working OK.  The guy who replaced the bad Compressor unit didn't fess up to a magnetic clutch problem, but ultimately I had a 'shut-off' of the A/C after five or ten minutes, which audibly included disengagement of the clutch. Consistently.

It's not fixed yet, but the symptoms include a surge in tachometer speed, and a simultaneous click, which was the disengaging of the compressor clutch.  Checking the pressure in the system, he said the pressure should remain below 280 (+/- 35) PSI; on my system, the pressure never went above that amount, while running engaged or unengaged..  So he felt there was an obstructed passage in the refrigerant line.  He purged that, and the problem persists.
He worked on it for two weeks, variously claiming it was fixed. Everything checked out... so he thought.  Finally, he talked with Toyota and they diagnosed the problem as a failure of the XLE's control head, the visible controller in the dash.  It was there the 'yellow' led would flash when the system 'failed'.  He's just replaced it, and four hours later, he said it hasn't failed... but when I started the car, it immediately failed and flashed.  I re-started it, and it continued for about 20 minutes, then, from that time on, it consistently fails about every 10 minutes.

I need to check if it IS the electro-magnetic compressor clutch - as they suggested., but something's gotta stop!  

I am quite sure this sounds like  Toyota TSB service bulletin EL0 -11-05  dated june 2003. If it is it is a very simple fix...replacing old  magnetic clutch relay with new part.  $20.00 or so from dealer.   Relay is under the hood in fuse box next to the battery. shown as MGT CL on schematic -check part number.  If the part number is 90987-02022, please replace the relay with the countermeasured relay P/N 90987-[bold]02028 Good  luck!!  hope this doesnt find you too late but it might have. Please let me know