ninsyoukoodo wo himitu ni suru.

It is read:

にんしょうコード を ひみつ に する。

• 認証コード = にんしょうコード
• 秘密 = ひみつ
• する = to do / to make

秘密にする means to keep secret or more literally to make something secret.

This uses the pattern:

X を Y にする = make X into Y / treat X as Y

So:

• 認証コードを秘密にする = keep the authentication code secret = make the authentication code secret

In natural English, keep ... secret sounds best.

を marks the direct object of the action.

Here, the thing being affected is 認証コード. It is the thing that is being made secret / kept secret.

So:

• 認証コード = authentication code
• を = marks it as the object
• 秘密にする = make secret / keep secret

That gives:

認証コードを秘密にする = keep the authentication code secret

In this sentence, に marks the resulting state.

In the pattern X を Y にする, Y にする means to make X become Y or to set X as Y.

Examples:

• 部屋をきれいにする = make the room clean
• 名前を英語にする = change the name into English
• 認証コードを秘密にする = make the authentication code secret

So 秘密に does not mean secretly here. It means into a secret state or as secret.

It is basically a noun, but it behaves like a na-adjective in many situations.

That is why you can see forms like:

• 秘密だ = it is secret
• 秘密の話 = a secret story
• 秘密にする = make it secret / keep it secret

So in this sentence, 秘密 is part of the pattern 秘密にする.

Japanese often leaves the subject unstated when it is obvious from context.

So 認証コードを秘密にする。 could mean different things depending on where it appears:

• in instructions: Keep the authentication code secret.
• as a policy: We keep authentication codes secret.
• as a personal decision: I will keep the authentication code secret.

Japanese does this very often. The listener or reader is expected to understand the missing subject from the situation.

By itself, する is the plain dictionary form, so it is not automatically a direct command in the same way as English Do it!

However, in certain contexts—especially rules, manuals, labels, or security instructions—the plain form can sound like an instruction:

• 認証コードを秘密にする。 = Keep the authentication code secret.

If you wanted other styles, you could say:

• 認証コードを秘密にしてください。 = Please keep the authentication code secret.
• 認証コードを秘密にしなさい。 = Keep the authentication code secret.
  (more direct, stronger)
• 認証コードは秘密にして。 = Keep the authentication code secret.
  (casual)

Yes, but the nuance changes a little.

• 認証コードを秘密にする

  • focuses on 認証コード as the object being made secret
  • matches the common pattern XをYにする

• 認証コードは秘密にする

  • makes 認証コード the topic
  • can sound like As for the authentication code, [we/you] keep it secret

Both are possible, but を is the most straightforward choice with this structure.

Sometimes, yes.

• 秘密にする = keep it secret / make it secret
• 秘密にしておく = keep it secret for now / keep it secret in advance / leave it secret

〜ておく often adds the nuance of doing something in preparation or maintaining a state.

So:

• 認証コードを秘密にする。 = Keep the authentication code secret.
• 認証コードを秘密にしておく。 = Keep the authentication code secret, and keep it that way.

The sentence you were given is perfectly grammatical, but in real-life advice, 秘密にしておく can sound a little more natural when talking about maintaining secrecy.

In many real-world contexts, 認証コード can be translated as either:

• authentication code
• verification code

The best English choice depends on the situation.

For example, if it is a code sent by text or email to confirm your login, English often says:

• verification code
• authentication code
• security code

So the Japanese is broad enough that the exact English wording may change depending on context.

Here are some common variations:

• 認証コードを秘密にします。

  • polite
  • I will keep the authentication code secret / We keep the authentication code secret

• 認証コードを秘密にしない。

  • plain negative
  • not keep the authentication code secret

• 認証コードを秘密にしません。

  • polite negative

• 認証コードを秘密にした。

  • plain past
  • kept the authentication code secret / made it secret

• 認証コードを秘密にしました。

  • polite past

These all come from conjugating する.