Most were interned and expelled. Robert A. Fearey, in a memoir ("My Year with Ambassador Joseph C. Grew, 1941-1942: A Personal Account", except here) recounts how the embassy staff and a few businessmen who had taken refuge there were immediately interned on Dec 7, and spent a reasonably pleasant time stuck in the embassy compound, save for a few golf trips to Tokyo courses, until they were expelled June 17. On the transport ship they met a variety of other Americans also being expelled, some of whom had fared rather less well:

The newsmen, who the Japanese assumed were all spies, had been held in closed confinement or prison, often in solitary, constantly interrogated and in many cases, tortured. (Later, on the ship, some of them demonstrated the “water cure” torture to which they had been subjected — some many times.)

...

Our newsman, Max Hill of AP, who had spent almost his entire internment in solitary under torture, said that if we did not depart, he would commit suicide. He clearly meant it and in fact did commit suicide some years later, perhaps due in part to what he had suffered in confinement.

...

U.S. Consul General Southard was one of the first to come on board. He had lost fifty-four pounds in confinement, and his clothes hung on him like sacks.

Fearey estimates 700 repatriates were on his ship from Japan, another 250 from Taiwan and Saigon, and an unknown amount on another ship from Singapore.

This was probably most of the American nationals in the country, with a few exceptions. Patrick James Byrne, a Catholic missionary, remained in Japan under house arrest rather than, well, actual arrest, due apparently to his reputation for charitable works.

There were a handful of naturalized citizens of American origin. Gwen Harold Terasaki, wife of Japanese diplomat Hidenari Terasaki, wrote a book about her experience in this category, "Bridge to the Sun" (later also a movie.) She had no trouble with imprisonment, and while you may say that as the wife of a fairly high official her experience may not be representative, she was also one of the very few people in this position.

Some 14,000 American civilians were captured in later stages of the war at Midway, Guam, Wake Island, the Philippines, merchant mariners, etc., and were mostly held as internees until the end of the war. These civilian internees were apparently treated somewhat better than military personnel; some 40% of POWs died while held, in contrast to 11% of civilians. (The numbers for those held by Germany were 1% and 3%, respectively.) I don't have a cause breakdown, but it's important to note that disease and transportation were much more dangerous in the Pacific, and a few specific events (like the sinking of prisoner transport ships and the "Bataan Death March") have an impact on those numbers besides the general treatment of the different classes of prisoner.