AI Damage2006 Yamaha Fjr1300ae: common problems
Owners of the 2006 Yamaha Fjr1300ae filed 16 complaints with NHTSA, most often about electrical system and engine and cooling. Details by component below, with sources.
Key figures
- Owner complaints
- 16
What fails most often
- 1 Electrical system 81% of all complaints
- 2 Engine and cooling 13% of all complaints
- 3 Powertrain 6% of all complaints
- Electrical system: 13 complaints (81% of all).
- Engine and cooling: 2 complaints (13% of all).
- Powertrain: 1 complaints (6% of all).
Symptoms owners describe
How many of the 16 NHTSA complaints mention each symptom (automatic count from complaint text; one complaint can mention several).
Components owners complain about
| Component | Owner complaints | involving a crash | Technical service bulletins (TSB) |
|---|---|---|---|
| Electrical system | 13 | 0 | 0 |
| Engine and cooling | 2 | 0 | 0 |
| Powertrain | 1 | 0 | 0 |
What owners report
Short excerpts of NHTSA complaints in the original wording. These are owner statements not verified by NHTSA; personal data removed.
A warning light came on "shift sh46" as I continued riding I attempted to shift gears with the paddle shifter (electric shift). The transmission would not shift. I attempted to down shift using the foot operated manual shift with the same results. The transmission was locked in 5th gear.
Yamaha fjr ae 2006. I purchased this bike in 2010 with only 3500 miles on it. Riding with friends we were about to enter a major interstate highway in dallas, tx. Upon giving the bike throttle the engine suddenly lost all power at about 50 miles per hour.
Vehicle was being ridding and the speedometer stopped working, abs and check engine lights started flashing and the gear indicator was also flashing. This is the ae model with electrical shifting. It was stuck in 5th gear and would not down shift.
I also cleaned off the connector plug that connects all the electrical connector terminals together due to corrosion and melted plastic stuck to it. Finally, I applied die-electric grease to the connectors to reduce corrosion and improve the connection between the connectors and the connector plug.
Left me stranded when it suddenly would not start. Symptoms included: 1.the fuel gauge bar display shows a full tank and the whole bar display is blinking on and off. 2. Horn won't work 3. The headlight high beam indicator is on, although the headlight is not on and switch is in the low position 4.
Tl contact owns a 2006 yamaha midnight venture 1300 (na). While driving 80 mph, the contact noticed oil spilling from the rear of the vehicle. The dealer stated that the oil seal failed and made repairs. The vin was unknown. The current and failure mileages were 12,000.
When owners complained
NHTSA complaints by filing year. The peak shows at what age the problems show up most.
Comparison
By complaint count this model year ranks 9,040 of 36,656 model years in the NHTSA data (top 25% most complained about).
What to check before buying
- Electrical system. Scan all modules, test the battery and alternator, inspect connectors near the impact zone.
- Engine and cooling. Radiator and fan after a frontal hit, coolant level and condition, overheating.
- Powertrain. Shift quality under load, harsh shifts, transmission codes, CV joints.
Questions and answers
What are the most common problems with the 2006 Yamaha Fjr1300ae?
Owner complaints to NHTSA most often mention: electrical system, engine and cooling, powertrain. Total complaints: 16. The most frequent symptoms in complaint texts: rust, corrosion (13%), warning lights, check engine (13%), fuel system, fuel smell (6%).
How many service bulletins (TSB) were issued for the 2006 Yamaha Fjr1300ae?
NHTSA lists 0 manufacturer service bulletins for this year. A bulletin tells dealers how to diagnose or fix a known issue; it is not a recall.
Should I buy a 2006 Yamaha Fjr1300ae from a US auction?
Owner complaints describe defects, not crash damage. Before bidding, check the components listed above and review the lot photos: VinWind builds a report of visible and hidden damage by VIN.
Other 2006 models
Read also
Sources: public NHTSA data (USA): service bulletins and owner complaints; YouTube: links to videos credited to their authors. Complaints are owner statements not verified by NHTSA, and describe defects rather than crash damage. Data updated 2026-11-05.