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McALLEN, Texas—Federal border agents say they will search for illegal immigrants at inland Texas checkpoints even during a hurricane evacuation, a plan state and local officials say could lead to disastrous delays and discourage some people from getting out.

Texas and federal officials have argued about the checkpoints roughly 75 miles from the border for years, but emergency managers only recently learned that the Border Patrol also plans to check the immigration status of people boarding buses at evacuation hubs in the Rio Grande Valley.

State and local officials are concerned not only about delays, but that the checkpoints could deter illegal immigrants from fleeing dangerous conditions.