Following Egyptian criticism of a U.S. decision to cut military and economic aid to Cairo after a crackdown on the Muslim Brotherhood, U.S. Secretary of State John Kerry stressed Washington was not severing ties with its long-standing ally.

The army-backed government insisted Egypt would not bow to U.S. pressure, with the cabinet saying it found the decision strange at a time when the country was "facing a war against terrorism."

However, U.S. Secretary of State John Kerry said Washington would consider resuming some of the aid "on a basis of performance" in following the interim government's "roadmap" that promises to lead to fair elections.

In Egypt's first public reaction, the Foreign Ministry said Thursday that the move, whether permanent or temporary, raised questions about Washington's commitment to supporting the Arab nation's security goals at a time when it is facing terrorist challenges, adding that it was wrong and ill-timed. The Foreign Ministry statement said Cairo was keen to maintain good relations with Washington, but will independently decide its domestic policies.

Washington faces a dilemma in dealing with its major regional ally; Egypt controls the strategic Suez Canal and has a peace treaty with Israel but its army overthrew in July the first freely-elected president, Islamist Mohamed Morsi, after mass protests against his rule. In some of the worst civilian violence in modern Egyptian history, security forces crushed protests by Morsi's supporters. However, militant Islamists, who have been attacking Egyptian forces in the Sinai peninsula for some time, have begun staging assaults in or near major cities including Cairo.

The United States said on Wednesday it would withhold deliveries of tanks, fighter aircraft, helicopters and missiles to Cairo as well as $260 million in cash aid, but left some other aid programs intact.

The Egyptian cabinet criticised the decision. "The government expressed the strangeness of the decision which was issued at such a vital time during which Egypt is facing a war against terrorism," it said in a statement said.

Kerry said Washington wanted to make certain the roadmap to new elections remained a primary goal of the interim government.

"The interim government understands very well our commitment to the success of this government... and by no means is this a withdrawal from our relationship or a severing of our serious commitment to helping the government," he told reporters on a visit to Malaysia.

Washington has long provided Egypt with about $1.55 billion in annual aid, including $1.3 billion for the military.

An Egyptian military source declined to give details on what effect the decision could have on military hardware as disclosing such information would harm national security.

The U.S. State Department has said it would continue military support for counter terrorism, counter-proliferation and security in the Sinai, which borders Israel. It will also continue to provide funding in areas such as education, health and private sector development.

Egypt's private, anti-Islamist leaning Tahrir newspaper was bolder in its criticism, with a headline proclaiming, "Let the American aid go to hell."

Israel fears that cutting aid to Egypt could affect the peace treaty between the two countries, signed in 1979, which brought Cairo into Washington's sphere of influence. Egypt is the second-largest recipient of U.S. aid after Israel. In recent months, Israel has tried to convince the White House that punishing Egypt for the latest violence between the government and protesters was secondary to preserving the peace deal.