This phrase is often used in Japanese conversations. In a nutshell, it means “thank you for waiting.” But more precisely speaking it is used for showing your respect for others and being sorry that you are late.
This phrase is usually used after you keep someone waiting for some reason or other. If you have to keep someone waiting on the phone, it will be polite for you to say, “omatase shimashita” when you start to talk again. When you have an appointment with your Japanese customer and you are late, you can say, “Sumimasen (sorry). Omatase shimashita.” At the beginning of a meeting, many people say, “Omatase shimashita. Kaigi (meeting) wo hajime masu.” That means “We are sorry to have kept you waiting. Now let’s start our meeting.”
At a concert or a movie theater, you may also hear this phrase used at the beginning, and very soon the concert or the movie will start. If you order something to eat or drink at a restaurant or a coffee shop, a waitress will bring what you ordered, saying “omatase shimashita.” When you are invited to dinner at your Japanese colleague’s home, you will be told just before dinner, “Omatase shimashita. Yushoku (dinner) no junbi ga dekimashita.” It means “Sorry to have kept you waiting. Dinner is ready now.”
Among family members or friends, you can use “omatase!” an informal way of saying “omatase shimashita.” For example, if you are late for a date, you can just say, “Gomen. Omatase.” “Gomen” is an informal form of “gomen nasai (I’m sorry).” Or if you have kept your partner waiting while you are using a toilet, you can also say when you come back, “Omatase!” So this phrase is sort of a social etiquette.