SACRAMENTO, Calif. - State and federal officials said Monday they were investigating the death of thousands of game fish in the Sacramento-San Joaquin Delta after a federal agency drained the water around a protected island during a levee repair.

Masses of fish could be seen floating in shallow water on Prospect Island, a 1,253-acre plot next to Sacramento's Deep Water Ship Channel that is administered by the U.S. Bureau of Reclamation.

The bureau stopped draining the remaining water behind the levee Monday and started removing the fish carcasses, spokesman Jeff McCracken said. The agency will add oxygen to the water in hopes of saving some of the remaining fish, he said.

"When we realized how many fish were there, we quit pumping," he said. "By then, we certainly, apparently, had passed the point of causing some fish loss."

The bureau had no estimate on the number of fish killed. Bob McDarif, owner of Cliff's Marina near the delta town of Freeport, estimated the number in the tens of thousands.

"It's like a disaster out there," he said.

The California Department of Fish and Game launched its own investigation Monday, focusing on how and why the fish died.

Although the fish deaths were on federal land, the striped bass, salmon, carp, bluegill and other game fish are considered public trust assets for the state. The results will be sent to state Attorney General Jerry Brown.

The Fish and Wildlife Service studied the potential effects of the drainage project on the delta smelt, which is protected under the California Endangered Species Act. That study showed the levee repair was likely to have no effect on the fish.

The Deep Water Ship Channel served as a conduit for a pair of humpback whales that made an unlikely journey inland from San Francisco Bay last spring.