US envoy Joseph Yun was summoned yesterday, the foreign ministry said, following his comments on the Sedition Act, which Prime Minister Najib Razak promised in 2012 would be binned.
Under intense pressure from ruling-party conservatives, however, Najib sparked an outcry late last month by saying it would be retained and even broadened.
The law is used overwhelmingly against opposition politicians and other regime critics.
"Malaysia is disappointed that the US Ambassador has chosen to highlight his unwarranted comments on the decisions of the government," the ministry said in a statement late Wednesday.
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Yun told a Malaysian news portal in an interview this week that the United States was "a little bit puzzled" by the reversal, saying Washington was "clearly paying attention to it".
The United States and Malaysia are seeking to bolster already solid ties, but Biden tweeted last week that the Malaysian government's use of the "legal system & Sedition Act to stifle opposition raises rule of law concerns".
Critics accuse Malaysia's ruling United Malays National Organisation (UMNO) of the calculated use of sedition charges to cripple the opposition, whose unprecedented recent electoral gains have shaken UMNO's 57-year hold on power.
Rights groups say the law allows virtually anything to be declared seditious, and have harshly criticised recent cases. Around three dozen people have been investigated, charged or convicted for sedition this year.
The embassy in October criticised the clampdown as threatening "rule of law and human rights".