In my article on Masahiro Tanaka, I speculated that Tanaka could see an average fastball velocity increase in the Majors because of some slow pitches that were tagged as fastballs by Yahoo!. The point was that the MLBAM tags seem to be superior to Yahoo! tags, so the fastball wouldn't actually be better, it would just look harder thanks to better labels, even if it is a slight increase. However, I have had a couple of readers on Twitter argue that pitchers who go from the NPB to the Majors have an increase in fastballs for whatever reason, unrelated to Yahoo's taggings. With Patrick Newman getting his NPB pitch data back online, this is something we can test. The data starts in 2009 and (currently) ends at 2012, so I looked through the player index, and looked for pitchers that pitched in the Majors as well as the NPB. I then removed every player that didn't play in the Majors and the NPB in consecutive years, because if there is a gap in years, then of course there will be drastic velocity changes. I only inputted the fastball velocities of the consecutive years. To use Yu Darvish as an example, I used just his 2011 NPB fastball velocity and just his 2012 MLB fastball velocity (there were a few pitchers that pitched in the MLB, then Japan, then the MLB again. For those pitchers, I used the first year of the second stint of the MLB as the velocity, along with the last year of the NPB stint). For the MLB velocity, I just used FanGraphs' Pitch F/X section for ease. I got 44 pitchers in my sample, not a large one, but one that should at least give us an idea of whether or not the hypothesis is correct.
The pitchers' average fastball velocity in the NPB was 89.04 MPH, while their average velocity was 91.22 MPH in the Majors, a gigantic 2.18 MPH difference. Of course, it isn't that easy. Many times, pitchers that were used as fringe relievers in the MLB were/are signed to NPB teams to be used as starters. If a pitcher pitches in relief in the Majors, and then as a starter in the NPB, then their average fastball velocity will be artificially down in Japan. For instance, in the Majors, the average velocity for starters is 91.4 MPH in 2013, and 92.9 MPH for relievers. This doesn't make up the whole difference, but it does possibly explain at least some of this. So I looked at the 44 pitchers again, and noted whether or not they changed from a starter to reliever or vise versa (if the majority of their outings were as a starter, I considered them a starter, etc.). Only 19 of them actually had role changes, with the other 25 staying the same.
Out of the 25 that stayed in the same role, their average NPB velocity was 90.02, while their average MLB velocity was 91.66 MPH. So there still seems to be a difference of about 1.5 MPH in velocity between the NPB and the Majors. The actual reason for this is unclear, and any theories put forth by me would all be speculation. Also, I should note that I didn't look at 2013 data, so there is always the chance that this has changed in someway, but for now, it appears that Yahoo's radar gun readings for the NPB are about 1.5 MPH slow compared to those of MLBAM's 50 foot release point designation.
There should be some caution exercised however, with a sample size this small, because there could be other factors driving the velocity changes. For example, two of the biggest velocity climbers from the NPB to the Majors were Hisashi Iwakuma and Chang-yong Lim, whose velocity increases could be explained, at least partially, from better health in the Majors (Iwakuma has batted shoulder problems in his career and was scarcely used in the first half of the season with Seattle, only to emerge in the rotation in the second half, Lim had Tommy John surgery in 2012, and his 2013 season is him coming off that. These injuries could have slowed down their fastballs in their last year of the NPB, while the MLB version of the pitcher is the healthy version). Pitchers like Yoshinori Tateyama, Colby Lewis and Yu Darvish actually saw a small decrease in velocity from the NPB to the Majors (all of them going to Texas), and Kam Mickolio has actually gained about a MPH in Japan after leaving the Majors.