There are far too many ways to apologize in Japanese. Even I, with my fascination both for the language and for apologies, find the sheer volume of apologies rather unnecessary. But of course, this is why we learn Japanese! It’s strange and interesting! ^o^
The apologies listed here are not just slight variations of the same phrase, such as “I’m sorry” and “I’m really very sorry.” Actually, every apology listed here has a totally different meaning and origin, and often can be used only in certain situations or by certain people.
Common Apologies
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sumimasen すみません
Most common apology. Means both “excuse me” and “I’m sorry.” Can be used in both formal and informal situations.
Past tense: sumimasen deshita すみませんでした.
The literal meaning is “It cannot be excused.”
Other variants: sumanai, suman, sumanu
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gomen nasai ごめんなさい
In casual situations, can be shortened to gomen (often gomen ne).
Unlike sumimasen, this is always used as an apology, never as an “Excuse me.”
It is a somewhat serious apology, but not used with superiors.
The literal meaning is “Ask for your pardon.”
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moushiwake arimasen 申しわけありません
A formal apology used with superiors.
Past tense: moushiwake arimasen deshita.
The literal meaning is “I have no excuse.”
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shitsurei shimashita 失礼しました
A formal apology, though less “heavy” than moushiwake arimasen.
Means both “excuse me” and “I’m sorry.”
Present tense: shitsurei shimasu! (“Excuse me, I’m coming in!” Used when entering a person’s place)
Short form: shitsurei (casual)
The literal meaning is “I have done something disrespectful.”
Also means “I will be leaving/Goodbye” (when exiting a person’s house/room/office)
Overly Formal Apologies
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owabi moushiagemasu お詫び申し上げます
Less formal: owabi shimasu / owabi (“apology”).
The literal meaning is “I humbly offer you my apologies.”
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osore irimasu 恐れ入ります
Think of this as more “Excuse me” (as in, “Excuse me, but I’m afraid I have to ask you to…”).
The literal meaning is “I am filled with awe/embarrassment (in your presence).”
Rude Apologies
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warui わるい (warii わりぃ)
Comes from the word for “bad,” warui 悪い.
Past tense: warukatta わるかった (“It was my bad”)
Short for ore ga warui (俺がわるい): “It’s my fault/It’s my bad.”
Casual and only used with familiars.
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suman すまん
Comes from sumimasen, mentioned above. Just a short, rougher way of saying it.
Various “Thanks/I’m sorry” Apologies
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osewa ni narimashita お世話になりました
“Thank you for your hospitality/generosity.” Literally means something like, “I have burdened you.”
sumimasen and warui are also commonly used in this “Thanks for helping me out/Sorry for troubling you” kind of way.
“I’m sorry I kept you waiting” Apology
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omatase shimashita お待せしました
Means, “I have made you wait.”

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These phrases can also be thought of as apologies:
Otsukare sama deshita.
Ojamashimasu.
Look them up
Yep, that’s correct. (Though those phrases are pretty circumstantial…) There are tons and tons of ways of apologizing… I’ve probably covered the tip of the iceberg only ;P