What we do know:
-Net Income for last nine months was 59.5B Yen
-This is forecasted to be 30B Yen in 3 months

Possible reasons for this are:
-Low expectations set so that they can easily meet them regardless of what happens with currency exchanges or the world economy
-Increased costs due to spending more on manufacturing
-R&D costs for Qualify of Life products or the successor to the 3DS or Wii U

Given the above, it is too difficult to determine if they are selling each Wii U at a loss or not. However, back in 2012, Reggie said that all it takes is one game to make them profitable:

http://www.gamesindustry.biz/articles/2012-11-21-reggie-it-only-takes-one-game-sale-to-make-a-wii-u-profitable

Back then, they were selling the Deluxe model for $350. It now sells for $300. My opinion is that in the last 2 years, costs for RAM / Gamepad screens / optical drives / CPUs should have gone down significantly. I would find it very difficult to believe that they would be worse off then they were 2 years ago (ie they should be making money from each console sold).

People need a reality check. The gamepad uses a naff resistive screen, cheap tiny capacity battery and a small pcb with no major components on. It's likely cost is $20 tops. You can get full tablets with capacitance screens, full logic boards with cpu/gpu/memory etc, incredibly more powerful and such tablets retail at $30-50. Plus they are made in smaller numbers. 

The reason the wii u costs Nintendo money is low sales. The amount of R&D, support costs, setting up the manufacturing line, halting the manufacturing line, marketing etc is not going to be paid back by the low sales rate. Having to re-package older stock to sell and having to deal with returns form retailers of unsold stock etc. 

It's hard to imagine the console and pad costs much to make and would probably be similar in cost to a hdd equipped 360 or PS3 however that said the wii u is often down in price below those consoles sometimes. In Europe the ps3 still easily outsells wii u and that is a market saturated with ps3s.

Let's not forget the wii u has lower spec memory than ps3 and 360 with only 12.6GB/s yes there is 4x as much though. 

The one thing that is costing Nintendo a lot in the wii u design is its slot loading drive. Remove this and perhaps replace with a top loading mechanism like ps3 and a lot of money will be saved. They could also bring back gamecube compatibility if they did this.

In cpu performance terms the wii u is much weaker than ps3 and 360. 

It seems whatever money Nintendo made on the wii they will end up losing on the wii u.

Yeah pretty soon the PS4 will be the same price as the Wii U.  It needed to be $150 a year ago.

I don't know if WiiU is being sold at a losso or not (although I'd expect it wasn't by now), but the main argument supporting this thread it's not true.

Accounting standards across the globe ditacte that you book the cost of WiiUs sold when and if they're sold. Therefore the "The manufacturing cost for much of the Wii Us sold so far this business year was already booked, making this year’s sales of Wii U exceptionally profitable on its books." argument is incorrect. WiiU don't book those costs on one year and then the profit from its sale the next year (I mean, if it takes you more than one year to sell it). What really happens is you pay for it but it remains in your balance as inventory until it's sold next year, only then the manufacturing cost will be booked.

Unless Japan has some really weird (and unlogic) account rules, that isn't the reason why WiiUs may or may not be sold at a loss. Only reason I see that happening is production costs become more expensive than what they were. That might do the trick.

Nintendo made a lot of mistakes with the WiiU, but there is no way the gamepad costs anywhere near $100.

Nintendo would've used custom hardware instead of PC hardware like PS4/X1 because it has a history of going to its own beat instead adapting.

They would've lost more

When I setup a repair with Nintendo, the cost was $100 for the GamePad and $10 for return shipping, plus taxes.  This requires that I ship a broken Gamepad to them.

When you lose it, it costs more ($140 + $5 shipping and taxes):

http://www.neogaf.com/forum/showthread.php?t=516246

Edit: CNN Report says it costs Nintendo $79 to make a Gamepad - http://www.gamespot.com/forums/nintendo-discussion-1000001/cnn-says-wii-u-basic-set-costs-228-to-make-29368526/

That is a little outdated. As someone stated earlier it probably cost them significantly less to make than almost 2 years  ago. 

This is what I was thinking as well.  If the WiiU Slim rumors are real, it could be a case of taking losses due to the initial switch, but making a more cost efficient console (and Gamepad) in the long run, which will hopefully show its effect sooner rather than later.  

My personal hope is that this is the case, and that this is also the reason why Mario Maker has been seemingly delayed from 1st half 2015 to the 2nd half, as I am still hopeful that the release of the game will coincide with a WiiU price drop to $249.

You do realize that Nintendo has "only" lost about $1b since fiscal 2011, right?  This was including having to cut the 3DS price from $250 to $170.  

Even with all of its losses and underperformance in the market, there is no way that WiiU will wipe out the massive profits that Nintendo made with the Wii.