By Greg Torode

HONG KONG (Reuters) - The top U.S. diplomat in Hong Kong warned on Thursday of a "big struggle" ahead to repair Washington's trust in the semi-autonomous Chinese territory after the flight of fugitive spy agency contractor Edward Snowden.

Speaking publicly for the first time since Snowden flew from Hong Kong to Moscow on Sunday despite a U.S. request to hold him to face charges of espionage, Consul General Stephen Young told Reuters that Washington's confidence was "shaken".

"My point is simple - I've spent three years working for good relationship between Hong Kong and the U.S. and we've had a loss of trust at this point," said Young, who is due to retire later this year.

Re-building that trust, he said, "is not going to be easy because you have President (Barack) Obama's administration just starting its second term so it is not like you can say: 'We'll wait for these guys to change'."

Young did not specify how any deterioration in ties would play out but added: "I'll say specifically in law enforcement co-operation - where we have a whole series of agreements, and protocols and practices - our confidence has been shaken."

The United States and Hong Kong have enjoyed strong ties under the "one country, two systems" system that has underpinned the former British colony since it was handed over to China 16 years ago.

U.S. multinationals have a strong presence in the city while U.S. warships are frequent visitors to its highly-strategic port on the South China Sea.

Young had repeatedly praised Hong Kong officials and the strength of their ties with the United States in recent speeches, before Snowden's revelations about the scope of Washington's electronic surveillance systems.

In Washington, officials have admonished China for letting Snowden escape, but Young said he was not so worried about the broader U.S.-China relationship, given its importance and opportunities for dialogue.

"But in U.S.-Hong Kong terms, it is a bigger struggle because people in Washington don't usually wake up thinking of Hong Kong but now they do, and it is in a negative sense," he said.

Young's comments come as Hong Kong and Washington officials continue a war of words over the back-room maneuvering ahead of Snowden's departure.

U.S. Department of Justice officials have accused Hong Kong of having feigned confusion over Snowden's middle name to avoid detaining him before he fled to Russia.

They were responding to statements from Hong Kong's Secretary for Justice Rimsky Yuen that his officials had to wait for clarification of Snowden's middle name and passport number in U.S. documents before detaining him at Washington's request.

The U.S. authorities used the middle name James in some documents for Snowden, while a U.S. Justice Department document referred to him as Edward J. Snowden, Yuen said.

But Hong Kong immigration records showed Snowden's name as "Edward Joseph Snowden."

"These three names weren't completely the same, so we felt that there was a need for clarification. Otherwise when we issued the provisional arrest warrant, it could have caused legal problems," Yuen said.

Before any clarification could be given, Snowden left. He has asked Ecuador for asylum and is now in a transit area of Moscow's Sheremetyevo airport.

(Additional reporting by Lavinia Mo; Editing by Raju Gopalakrishnan)