Foreign Minister Sayyid Hamid Albar was quoted by the country's Sunday Star as saying Malaysia was being unfairly targeted because it was a Muslim country and lumped together with countries such as Iran, North Korea and Libya.
"Malaysia is not even in that league of countries which have nuclear proliferation capabilities. It is totally uncalled for," he said.
Sayyid Hamid said Bush had ignored Malaysia's cooperation with the United States on issues such as the international fight against terrorism and the non-proliferation of nuclear weapons.
"We are very disappointed," he said.
"What he (Bush) said was very misleading. We will write to the embassy soon to communicate our displeasure and our unhappiness."
In a speech at the National Defence University in Washington last Wednesday, Bush repeated charges that centrifuge parts for Libya's nuclear weapons uranium-enrichment programme were manufactured in Malaysia.
He was seeking global support for tighter curbs on nuclear know-how, taking aim at North Korea, Iran and black market sales by Pakistan's disgraced scientist Abd Al-Qadir Khan.
Pakistani scientist AQ Khan
admitted to black market sales
The company involved, Scomi Precision Engineering (SCOPE), has admitted making parts found on a ship heading for Libya, but said it did not know their final destination and believed they were for the oil and gas industries.
The company is controlled by Prime Minister Abd Allah Ahmad Badawi's son, Kamal al-Ddin.
Abd Allah has ordered a police investigation into the case and police said later initial investigations had revealed the company did not commit any criminal offence.