The NSA whistleblower Edward Snowden has flown out of Hong Kong, where he had been in hiding since identifying himself as the source of revelations on US surveillance programmes, despite a US request for his arrest.

The 30-year-old had previously said he would stay in the city and fight for his freedom in the courts. But the Hong Kong government confirmed that he left on Sunday, two days after the US announced it had charged him with espionage, saying documents filed by the US did not fully comply with legal requirements.

It also said it was requesting clarification from Washington on Snowden's claims that the US had hacked targets in the territory.

Snowden had been at a safe house since 10 June, when he checked out of his hotel after giving an interview to the Guardian outing himself as the source who leaked top secret documents.

Hong Kong's decision to allow him to leave comes a day after the US sought to turn up the pressure on the territory to hand him over, with a senior administration official telling the Washington Post: "If Hong Kong doesn't act soon, it will complicate our bilateral relations and raise questions about Hong Kong's commitment to the rule of law."

Sunday's statement from the Hong Kong authorities said: "Mr Edward Snowden left Hong Kong today [June 23] of his own accord for a third country through a lawful and normal channel.

"The US government earlier on made a request to the HKSAR [Hong Kong special administrative region] government for the issue of a provisional warrant of arrest against Mr Snowden. Since the documents provided by the US government did not fully comply with the legal requirements under Hong Kong law, the HKSAR government has requested the US government to provide additional information so that the Department of Justice could consider whether the US government's request can meet the relevant legal conditions.

"As the HKSAR government has yet to have sufficient information to process the request for provisional warrant of arrest, there is no legal basis to restrict Mr Snowden from leaving Hong Kong.

"The HKSAR government has already informed the US government of Mr Snowden's departure.

"Meanwhile, the HKSAR government has formally written to the US government requesting clarification on earlier reports about the hacking of computer systems in Hong Kong by US government agencies. The HKSAR government will continue to follow up on the matter so as to protect the legal rights of the people of Hong Kong."

According to the South China Morning Post, Snowden boarded an Aeroflot flight to Moscow, although the newspaper said Russia was not his ultimate destination. It suggested he might go to Ecuador or Iceland – having cited the latter as a possible refuge in an interview with the Guardian.

However, reports from Moscow indicate that Havana would be his next port of call, with the ultimate destination either Caracas in Venezuela or Quito in Ecuador.

The South China Morning Post claimed he took off from the airport at 10.55am on flight SU213 on Sunday morning and was due to arrive at Moscow's Shermetyevo International Airport at 5.15pm [local times].

It said the Russian embassy in Beijing would neither confirm nor deny he was on a flight to Moscow and the Russian consulate in Hong Kong declined to comment.

Dmitry Peskov, spokesman for Russian president Vladimir Putin, said: "I don't [know if he's planning to stay in Moscow]. I heard about the potential [arrival] from the press. I know nothing."

On whether Moscow would still consider a request for asylum from Snowden: "Every application is considered so it's standard procedure … We are not tracing his movements and I know nothing."

US authorities could not be reached for comment.

WikiLeaks tweeted to say that it had "assisted Mr Snowden's political asylum in a democratic country, travel papers and safe exit from Hong Kong".

On Friday, an Icelandic businessman linked to WikiLeaks told Reuters he had prepared a private plane for Snowden's use if the government was willing to give him asylum.

"A private jet is in place in China and we could fly Snowden over tomorrow if we get positive reaction from the interior ministry. We need to get confirmation of asylum and that he will not be extradited to the US. We would most want him to get a citizenship as well," said Olafur Vignir Sigurvinsson, a director of DataCell, which processed payments for WikiLeaks.

The Icelandic government has declined to say whether it would grant asylum to Snowden and pointed out that he would need to apply in person.

Snowden has said he did not travel direct to Iceland from the US because he feared the small country could be put under pressure by Washington.

Lawyers have said the legal battle for Snowden's surrender could last for years, particularly if he argued that he should not be returned because his offence was political. But they had also warned that in the long run he was unlikely to prove successful.