Under the new policy, the US Immigration and Naturalisation Service (INS) will routinely fingerprint, photograph and question potential entrants, checking their pictures and prints against criminal and terrorist databases.
The policy is aimed at preventing a repeat of the security lapses which allowed the 11 September hijackers to live undetected in the US for so long.
Malaysian Prime Minister Mahathir Mohammad said the measures represented "anti-Muslim hysteria" in the US.
Pakistan's foreign ministry spokesman said it was unfair given his country's support for the US-led "war on terror".
The Arab-American community in the US has said people will be targeted on the basis of their race and religion.
The US Justice Department has also issued a directive that anyone who has frequently visited the Middle East, North Africa, Cuba or North Korea can be taken aside too, if they do not have what it calls a credible explanation for their trip.
The measures, introduced nationwide on Tuesday, could potentially apply to any of the 35 million foreign visitors who come to the United States every year.
But all citizens of Iran, Iraq, Libya, Syria and Sudan will be targeted, and visitors - especially men - from other Muslim and Middle Eastern countries may also be subject to the new measures.
Muslims 'labelled'
Dr Mahathir said he was upset at the American measures.
"Because of the acts of a few people, the whole Muslim world seems to have been labelled," he said.
Those affected by the new policy
All nationals of Iran, Iraq, Libya, Sudan and Syria
Non-immigrant foreign nationals who present an elevated national security risk
Foreign nationals identified by INS inspectors
On 16 September, Dr Mahathir's deputy Ahmad Abdullah Badawi was asked to remove his belt and shoes at Los Angeles airport before being allowed to fly on to New York.
Pakistan's foreign ministry spokesman, Aziz Ahmed Khan, said the decision to register all Pakistani men between 16 and 45 entering the United States was unfair and wrong.
Mr Khan said the Pakistani Government had expressed its concern to the American authorities and would continue to take it up.
The BBC's Susannah Price says Islamabad is particularly annoyed because it sees itself as a close ally of the United States, unlike other countries affected, such as Iran, Iraq and Libya.
Formal registration
Since the 11 September attacks, many Middle Eastern and North African visitors to the US have been taken to one side for questioning.
Now those aged 16 to 45 deemed an "elevated security risk" will be formally registered by the authorities.
They will then have 30 days to say where they are living, working or studying.
BBC New York correspondent Jane Standley says it will be hard for the US bureaucracy to keep up with the new regulations, with more than 350 air and sea ports as well as land borders to monitor.