The Philippines and Vietnam have objected that the map shows disputed maritime regions as belonging to China. India has also complained over the map's depiction of its northern border with China and retaliated by issuing Chinese citizens visas embossed with New Delhi's own maps.
State Department spokeswoman Victoria Nuland told a news briefing it was up to countries to decide what their passports look like and the US would still accept the Chinese one as a legal document.
But she added: "That's a different matter than whether it's politically smart or helpful to be taking steps that antagonise countries."
She said it was unhelpful for creating an environment for resolving the territorial disputes.
The US intervention won't be welcomed by Beijing, which regards as meddling Washington's advocacy for peaceful settlement of the conflicting claims in the South China Sea, a potential regional flashpoint. The US has no territorial claim itself but says it has a national interest in the stability of a region vital to global trade.
Taiwan has also condemned the map, which is printed on inside pages of the passport. Taiwan is self-governing but Beijing claims it as part of China.
The map shows an outline of China and includes Taiwan and the sea, hemmed in by dashes. Chinese official maps have long shown the same, but this is viewed as particularly provocative since it requires other nations to stamp it.