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2003 R6 Error code 46

29990 Views 25 Replies 14 Participants Last post by  jthomm32
my check engine light came on today I am getting error code 46, I just bought this bike a couple months ago and this is the first time I have had this problem, after doing a little search I read that it could simply be a loose fly wheel bolt, where and how do I tighten this, if I could go without taking it to the shop it would be great.

Thanks for your help!!!!
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Workin on it... Give me a couple mins... I'll be right back with your answer .
I can't seem to get the page to load up. What kinda of work have you been doing to your bike lately? Anything to do with the sparkplugs and coils? Have you had the gas tank off at all, or the airbox out of it.? Let me know.
I'm working on finding the error code page though... Bear with me.
I still haven't got my hands on the actual service manual, but everything that I can find points to the Rectifier. You may need a new one bro. I will continue to dig. If I find anything else, I'll let you know. If you find out, let me know.

I would also check the connector for the rectifier before you flip out and go buy a new one.
nope I haven't taken anything apart or done anything, I found that error code 46 is

( error 46 Power supply to the FI system relay is
not normal. Open circuit in wiring harness. (red / white line)
Malfunction in “CHARGING SYSTEM”. — )

and that this was a common problem and that the fix is usually tightening the flywheel
alright then.
Hey where did you find that error code? My bike is having the same problem, but what does tightening the flywheel have to do with Open circuit in wiring harness. (red / white line)
Malfunction in “CHARGING SYSTEM”. — )
Hey where did you find that error code? My bike is having the same problem, but what does tightening the flywheel have to do with Open circuit in wiring harness. (red / white line)
Malfunction in “CHARGING SYSTEM”. — )
:werd what does that have to do with electrical? and where did you hear that tightening the flywheel bolts are a common problem for this code?
hey i am currently having the same problem my battery starts off at 12.8 than drops down to 11.8 after running awhile i used a mutlimeter to test the stator and it seems to be working i also checked the plug going into the regulator rectifier and it is getting a reading also could it be i have a ground wire off or something?
my fiends FZ6 got the same problem. we put a new battary on it too. but after riding on heavey electrical load. ex: in traffic where the fan runs constantly. bike would die and code 46 would pop up. cant seems to solve the problem.
same bike.. same problem, already fixed it once. It is definately your voltage regulator rectifier and/or your stator. i would start by checking your rectifier harness. the rectifier is located under the gas tank, you can see it by taking off the seat and its screwed into your battery holder. when i checked mine it was completely toasted and all wires melted together. from what i read this is usually the problem, caused by excess heat and exposure to the elements. I went ahead and re did my own harness by buying connectors from autozone and soldering my own connections. But after two weeks my bike is back with error code 46, dead battery, and no burned harness or anything. If your in my position, you now need to check resistances on all 3 white wires coming from the stator to the R/R, for me the stator looks fine so i am about to order a new R/R as its the only thing i can think of that is causing this, i will also be replacing my battery as its been completely drained about 4 times because of this stupid voltage regulator so i figure its fried.
r6 voltage regulators are placed in a very bad spot, i would recommend finding a better ventilated area to install it if you decide to buy a new one, i really hope this gets my bike working smooth.
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Have you had any luck with this lately? Tonight my bike died and I pop started it and took it home and got code 46 also. I also read on an r1 forum that there was a service bulletin for the flywheel coming loose on 03 r6's causing the charging system to fail? I also heard about the rectifier frying, but I want to make sure before I start tearing things apart. If you have any information, it would be much appreciated. I really don't feel like paying for this if it was already recalled.
after a quick and simple install of my new R/R, and re doing the wireing all the way up from the stator to the R/R, its been over a month and no problems. I also changed the position of the R/R to directly under the battery so its hanging out getting air, i also made a lil heat sink for it out of aluminum using the idea from a post i read. Did not ever even replace battery and have not had any electrical issues, and i just added custom blinkers and HID's.
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I got mine tested and the rectifier is what took a shit. Replaced it and now I'm good to go. Also, I've been wanting to do HID's in mine as well, but I didn't want to do ebay kits, where did you get yours?
ddmtuning.com could not be any happier, i bought the 35w 8k kit, has awesome slight blue tint.
hate to bring this up from the dead, but my bike is back to error 46.
I dont get it, if this bike is gonna be frying RR's every 3 months, i wont have it much longer..

anyone keep having issues with the charging system also?
I moved my RR to the bottom of the battery tray have u tried this yet.
error code 46 means you have Valentino Rossi's practice bike. It also has about 46 extra HP and 46 more pounds of torque. You can also run the quarter mile 4.6 seconds faster and shave 46 seconds off your fastest lap time at any race track. I'd sell it...its a piece of junk. Error code 99 is way better :lmao
Try replacing or tightening the fly wheel that was the case with my buddies bike, after we replaced everything on it twice. I had a spare engine and we threw the magnet off that and on to the other bike and it worked like a charm, i guess it could have been loose but it was also in a lay down and the mechanic we finally took it to said a hard hit can screw with the magnets on the fly wheel. ps you will need a puller to take it off.
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