Deputy Prime Minister Abdullah Ahmad Badawi had to take off his shoes and belt in Los Angeles last month despite holding a diplomatic passport.
"The US embassy sincerely regrets any inconveniences or inappropriate treatment that senior Malaysian Government officials may have experienced during their visits to the US," the Kuala Lumpur embassy said in a statement on Wednesday.
The apology followed an outcry in Malaysia after Mr Badawi's experience was made public this week.
Prime Minister Mahathir Mohamad on Tuesday accused the US of "anti-Muslim hysteria".
Boycott call
Malaysian anger has been compounded by new security measures at US airports which means Malaysians can be photographed and fingerprinted on arrival and matched against terrorist databases.
Immigration officers can register certain visitors from selected Arab and Muslim countries including Malaysia, Iran, Iraq, Libya, Syria and Sudan.
Dr Mahathir has said he is very upset at the new measures which he says labels all Muslims as potential terrorists.
Following the news of Mr Badawi's experiences in LA, a former newspaper editor revealed he recently had to go through a three-hour interrogation by security officials at Des Moines International Airport in Iowa.
Kadir Jasin, writing s column for a business monthly, says he plans to boycott travel to the US and is urging other Malaysians to go elsewhere to holiday or study.
Mr Badawi, who is set to succeed Dr Mahathir when he retires next year, was on his way to New York to address the United Nations general assembly when he was stopped at LA airport. He has played down the incident.
"All of us had to undergo the same security checks, even the pilot," he told the Star newspaper.
Malaysia has arrested more than 60 suspected militants in the past year, who are mostly accused of trying to set up an Islamic state in South East Asia.
One of the suspects is alleged to have links with the al-Qaeda network blamed for the 11 September attacks on the US. Malaysian officials accuse Yazid Sufaat of having direct contact with two of the hijackers.