Ricardo Ramirez alleged that former Attorney General Janet Reno and former INS commissioner Doris Meissner conspired with underlings to destroy evidence of bias and threaten agents if they broke ranks.
U.S. District Judge Alan Gold agreed with a federal magistrate's decision that the lawsuit should be dismissed on the grounds that it was an employment dispute governed by civil service law.
Ramirez, who is of Mexican-American descent, said he has received official and anonymous threats since reporting the alleged bias.
Gold wrote that while the "court is troubled by the allegations contained in Ramirez's complaint, which reveal an elaborate conspiracy to penalize a federal employee for truthfully providing information, it cannot supplant the method created by Congress for such federal employees to redress their grievances."
Ramirez said he saw evidence of bias at the Miami INS office around the time of the raid, including a slashed Cuban flag, a Miami seal bearing the words "Banana Republic" and pictures of Elian that said "Kick me."
Judicial Watch chairman Larry Klayman, Ramirez's attorney, said he intends to appeal.
Charles Miller, a Department of Justice spokesman, said the department was satisfied with the judge's order.
Elian's Miami relatives unsuccessfully fought in court to keep Elian in the United States after his mother drowned during a boat crossing from Cuba to Florida in November 1999. The boy returned to Cuba with his father the following June. [End]