From one of the previous 15 (really) threads on the same topic:
The error is intentional to make sure the manufacturer can use different sources of tires and still meet the United Nations agreement on accuracy. Vehicle manufacturers who spec only one or two tire models as standard equipment (Harley for example) are typically more accurate because they only have to make sure the calibration never goes low. (They will still be slightly high because new vehicles can absolutely never be low.)
The following is the source of the rules:
Vehicles conform to United Nations Requirement #39, which is called: UNIFORM PROVISIONS CONCERNING THE APPROVAL OF VEHICLES WITH REGARD TO THE SPEEDOMETER EQUIPMENT INCLUDING ITS INSTALLATION (See:
http://www.unece.org/fileadmin/DAM/trans/main/wp29/wp29regs/r039r1e.pdf) The speedo accuracy may be found on Page 8, Paragraph 5.3, which states:
The speed indicated shall not be less than the true speed of the vehicle. At the test speeds specified in paragraph 5.2.5. above, there shall be the following relationship between the speed displayed (V1 ) and the true speed (V2).
0 ≤ (V1 - V2) ≤ 0.1V2 + 4 km/h
This formula is where your speedo INaccuracy is designed in. Your dealer can't do a thing about it. Neither can Yamaha USA (or Canada/UK/AUS/etc) as an importer, which really is just a subsidiary that buys vehicles from a foreign manufacturer and then resells/distributes them. The manufacturers for the US also have to account for NHTSA coming in with a measurement error, keeping with the requirement to NEVER display less than actual speed.