US envoy Stephen Young also said China was guilty of "misbehaviour" over the former NSA contractor's abrupt departure from Hong Kong last Sunday, but said the territory itself would bear the brunt of Washington's displeasure.
Hong Kong officials say that a US request a week ago asking for Snowden to be detained was riddled with clerical errors, and there was no legal basis to stop him flying to Russia.
But Young, who retires at the end of July, said Washington was busy "dotting the i's and crossing the t's" in what it took to be a normal process of communication under the two sides' extradition agreement.
"They've been throwing out some arguments as to what was going on. But frankly I don't think we had a good-faith partner throughout that process," the consul-general told foreign reporters, accusing Hong Kong of "obfuscating" the real issues.
Snowden abandoned his high-paying job as an IT technician contracted to the National Security Agency and went to Hong Kong on May 20.
He then began issuing a series of leaks on the NSA's gathering of phone call logs and Internet data, triggering concern from governments around the world.
US administration officials allege that Hong Kong, backed by Beijing, wanted to remove an irritant and was bent on letting Snowden leave regardless of the US indictment.
Young said the city's handling of the case had left a "very bitter taste in American policymakers' mouths" and "injected a tone of distrust that I think is going to take time and effort to erase".
But Hong Kong could not expect to continue being treated as a special case lying at one remove from the rest of China, the envoy said.
"I certainly personally would hate to see a situation where we decide to treat Hong Kong like just another part of China. So the question is how do we get out of this, and I don't know."
On Tuesday, Hong Kong's Secretary for Justice Rimsky Yuen said US suggestions that the government connived at Snowden's departure were "totally untrue".
Lawmakers from both sides of the city's pro-democracy and pro-Beijing divide have also lashed out at the US accusations.
One told South China Morning Post that the US arrest paperwork was "sloppy", and another argued that Washington was "shameless" after Snowden alleged a far-reaching programme of US cyber-espionage in Hong Kong.
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