Egypt was particularly upset over a November 2 meeting in Washington between US President Barack Obama's national security advisers and a group of US foreign policy analysts who are pushing for reforms in Egypt.
The bi-partisan group was described as "the same type of groups that want to spread chaos in the Middle East."
On Monday, the State Department called on Egypt to hold a free election and allow international monitors to observe the November 28 parliamentary poll.
Past elections have been marred by violence and irregularities, and Egyptian rights groups say the vote has already been compromised by the arrests of many opposition activists.
Rights groups also say rights violations such as torture are routine in the country, which the government denies.
"It is as if the United States has turned into a caretaker of how Egyptian society should conduct its own politics," the foreign ministry statement quoted an unnamed official as saying. "Whoever thinks that this is possible is deluded."
The statement said the tradition of mutual respect would be honoured as long as the United States reciprocated in it.
Egypt, one of two Arab countries that have diplomatic relations with Israel, receives billions of dollars in US foreign aid.
It has played an important role in mediating between Israelis and Palestinians, a priority of Obama's administration.
Egyptian foreign ministry spokesman Hossam Zaki alluded to the strategic relationship in a television interview in which he warned that "if (the US) intends more of this, Egypt, which takes strong stances, will have a clear position."
He was responding to a question on whether the government would take further steps after releasing the statement.
"Neither party has an interest in escalation because the US-Egyptian relationship remains important for regional stability," Zaki said.
While never under serious threat, ties underwent a chill in the past decade after then president George W. Bush pressed Egypt to hold free elections and release dissidents.
Obama restored warmth to the relationship and was seen to have shied away from Bush's robust democracy advocacy.
The new tone, analysts say, partly reflects US uncertainty about Egypt's future.
The country will vote for a president next year, and it is still unknown whether 82-year-old incumbent Hosni Mubarak, in power since 1981, will seek another term.
His successor will probably come from the ruling party or the military, and other contenders are not expected to have a serious chance.
"Like many people in Egypt, the Americans are concerned about where this country is heading," said Issandr ElAmrani, a Cairo-based analyst.
Michele Dunne, who attended the November 2 meeting, said the administration was still trying to form a coherent policy on democracy and human rights after initially distancing itself from Bush's agenda.
"In its first year the Obama administration said almost nothing about these rights. Human rights groups were upset about that, and not primarily about Egypt," said Dunne, a former State Department Middle East specialist and analyst with the Carnegie Endowment for International Peace.
"Egypt's case is before them right now because of the elections and probably an impending leadership succession," she said.
"There is a growing concern that we have this ally and we want them to be our ally, but think that the way to promote greater stability is not to prevent all change," she said.
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