The embassy was first closed Friday as part of an ongoing process to close the mission at least one day a week.
The one-day closures have been taking place since May 15, when the U.S. State Department issued a beefed-up terrorism advisory for American citizens warning against travel to the East African nation.
But following a U.S. Defense Department (search) terrorism alert Friday that raised the threat level in the country to "high," officials decided to keep the embassy closed on Monday and Tuesday.
Embassy officials, who do not ordinarily publicly discuss security matters, would not say if the embassy would be closed again.
Kenya has been the scene of two terrorist attacks -- both blamed on Al Qaeda -- in the last five years, and recent intelligence has raised fears of another attack.
On Nov. 28, a car bomb killed at least 10 Kenyans and three Israelis at a hotel north of the Indian Ocean port of Mombasa. Minutes before that attack, assailants unsuccessfully tried to shoot down an Israeli charter jet with shoulder-fired missiles as it was taking off from Mombasa's airport.
In 1998, the U.S. Embassy was blown up, killing 219 people, including 12 Americans.
A Kenyan court on Tuesday charged four men with 13 counts of murder Tuesday in connection with the November attack.
Following the Pentagon alert, Kenya banned all air traffic between the East African country and neighboring Somalia.
Somalia, a Muslim nation that has not had an effective government since 1991, is believed to be a transit point and staging ground for Al Qaeda operatives working in eastern Africa.