Netanyahu's decision to speak at a joint session of Congress on March 3 "injected a degree of partisanship" between the nations and is "destructive to the fabric of the relationship," Rice said.
Rice's comments are the Obama administration's strongest criticism of Netanyahu's speech.
"The point is, we want the relationship between the United States and Israel to be unquestionably strong, immutable, regardless of political seasons in either country, regardless of which party may be in charge in either country," Rice said on the PBS show "Charlie Rose The Week."
She added that the United States will continue working to maintain a strong relationship with Israel.
Netanyahu is scheduled to speak about the dangers of a nuclear-powered Iran to a joint session of Congress two weeks before elections in Israel. The White House wishes to seek diplomacy with Iran over its nuclear program, while Netanyahu supports more sanctions on Iran.
Some pro-Israeli leaders urged Netanyahu to cancel his controversial speech to Congress, while some condemned the possibility of a speech boycott.
Republicans did not consult with the Obama administration about Netanyahu's visit to Congress. President Barack Obama is not scheduled to meet the prime minister.
Israel's Central Election's Committee recently announced that Netanyahu's speech to the U.S. Congress will receive a five-minute delay when it is broadcast in Israel, in an effort to allay fears of possible electioneering.