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A: あした 東京【とうきょう】へ 行き【いき】ます。
B: 何【なん】で 行き【いき】ますか。
A: 新幹線【しんかんせん】で 行き【いき】ます。
B: 一人【ひとり】で 行き【いき】ますか。
A: いいえ、会社【かいしゃ】の 人【ひと】と 行き【いき】ます。

(original page)

The example given here (from Minna no Nihongo 1) uses 「何でいきますか」 as "In what means did you go?" but from my understanding, if you wanted to say "Why did you go?" it would be exactly the same phrase.

If you just look at the first 2 phrases in this example, it isn't necessarily clear which person B is asking for. Person B could easily be asking person A why he is going to Tokyo rather than how (in this case)

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    「何でいきますか」 as "In what means did you go?" ... "Why did you go?" <-- "did you" should be "will you", right? It's いきます, not いきました. They're talking about あした !
    – Chocolate
    Sep 27 at 5:48
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The short answer is that both meanings are applicable and the only way to know is from context.

The problem here is that in spoken language, なに tends to be shortened into なん, such that the two meanings "by what means" and "for what reason" overlap. If one wants to be clear, one should say なにで when referring to "by what means", and in writing it is good to not use the kanji in this case. In written text, they should be distinguished (なに for "by what means") but since the text in your image refers to spoken language, it is shortened there.

I remember having the same question when I first started learning Japanese many years ago, also with that book. However, I cannot really recall having heard it used in the sense of "by what means" in real life, people will instead say なに. Perhaps there is a regional difference, I've mostly lived in Fukuoka.

Here is some data from a survey I found: http://nhg.pro.tok2.com/reserch/reserch1-3.htm

The survey asks "Do you use なに or なん when asking about commuting method?". In total, 71.4 % prefers なに. In 近畿{きんき} more people prefer なに than in 関東{かんとう} , although only 105 people were interviewed so no strong conclusions can be drawn from this survey.

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