Secretary of State Colin Powell said he fully supported Mr Bush's targeting of Iran, Iraq and North Korea as countries thought to be developing weapons of mass destruction.
He told US television the three countries "continue to act in ways that just are inconsistent with the expectations of the 21st century and are hindering our campaign against terrorism".
In a separate interview, Defence Secretary Donald Rumsfeld accused Iran of letting al-Qaeda and Taleban members escape from Afghanistan.
And National Security Adviser Condoleezza Rice urged Americans to devote their energy to containing the threat posed by arms proliferation.
America's singling out of the three led to angry responses from their governments, and also unease among US allies that it was considering widening the scope of its campaign against terrorism.
Iran criticised
Speaking on the US television network ABC, Mr Rumsfeld said Iran had given Washington's opponents free passage across the Iran-Afghanistan border after the fall of the Taleban.
BBC Washington correspondent John Leyne says the main purpose of the remarks is not to threaten war but rather to increase Iran's diplomatic isolation.
Iran has traditionally been an enemy of the Taleban, though it has always had strong links with parts of Afghanistan.
On Friday Ayatollah Ahmad Jannati, head of the powerful Guardian Council, said Iran and the Taleban "hated each other and had nothing in common".
But Mr Rumsfeld said that Iran, unlike Pakistan, had failed to put troops along its border with Afghanistan to prevent al-Qaeda and Taleban fighters from escaping.
"There isn't any doubt in my mind that the porous border between Iran and Afghanistan has been used for al-Qaeda and Taleban to move into Iran and seek refuge," he said.
But our correspondent says Secretary Powell failed to endorse all of Mr Rumsfeld's accusations.
New front fears
There has been mounting international concern about President Bush's grouping together of Iran, Iraq and North Korea.
Prime Minister Mikhail Kasyanov of Russia, which sees all three as falling within its sphere of influence, questioned whether there was evidence to label the three an "axis of evil".
There have been angry responses from the countries themselves, while several allies of the US have expressed fears that it is preparing to open a new front in its war against terrorism.
Meanwhile the British Foreign Secretary, Jack Straw, has said Britain will continue its dialogue with reformists in Iran, while sending what he called "strong messages" to hard-line elements within the government.
The European Union also has a policy of engagement with the authorities in Tehran, which the BBC's Middle East analyst Roger Hardy says they have no intention of abandoning.