(Reuters) - A barrier that holds back the Mississippi River near its confluence with the Missouri River was breached on Tuesday, sending water two miles inland, threatening homes and prompting new warnings for residents to leave the area.

The breach of the levee was near West Alton, Missouri, just north of St. Louis, and threatened more than 40 homes, officials said.

About 300 West Alton residents were asked to leave their homes on Monday night after a temporary flood barrier failed in a different location on the sparsely populated peninsula formed by the connection of the two rain-swollen rivers.

Heavy rain has swelled rivers in the U.S. Midwest, with some areas well beyond flood stage, and forced officials to close eight locks and the Port of St. Louis along the Mississippi River, a major shipping artery.

The breach of the levee on Tuesday was estimated at up to 150 feet and river water quickly pressed two miles inside the levee, said Colene McEntee, a St. Charles County, Missouri, spokeswoman.

The National Weather Service issued a flash flood warning, saying the breach was just below the Melvin Price Lock and Dam.

The Mississippi River was about 13 feet above flood stage at the lock on Tuesday afternoon. The Missouri River was more than 12 feet above flood stage at St. Charles and receding slowly.

"It doesn't look like they are going to go up any higher than they already are," said Mark Fuchs, a hydrologist at the National Weather Service office in St. Louis.

The breaks could actually lower the river levels a little bit near the confluence and slightly at St. Louis, he said.

McEntee said emergency efforts to reinforce or encircle trouble spots with sandbags and erect barricades helped hold back the Mississippi River on Monday after the temporary barrier failed. No residents had sought shelter, she said.

(Reporting by David Bailey and Karl Plume; Editing by Cynthia Johnston and Bob Burgdorfer)