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The USS Lassen transits in formation in waters east of the Korean Peninsula, March 12, 2015. U.S. Navy/Mass Communication Specialist 1st Class Martin Wright/handout via Reuters

By Andrea Shalal, Matt Spetalnick and David Brunnstrom

WASHINGTON (Reuters) -- The U.S. naval challenge to China's territorial assertiveness in the South China Sea this week came after months of frustration within the Pentagon at what some defense officials saw as unnecessary delays by the White House and State Department in approving the mission.

As early as mid-May, the Pentagon was considering sending military aircraft and ships to assert the principle of freedom of navigation around China's artificial islands in the Spratly archipelago after Defense Secretary Ash Carter requested options to respond to their rapid construction.

That patrol eventually took place on Tuesday when the USS Lassen, a guided-missile destroyer, sailed within 12 nautical miles of Subi Reef, triggering an angry rebuke from China and threatening to ratchet up tensions between the world's two biggest economies.

An intense, prolonged internal U.S. debate over the patrol revealed by Reuters' reporting appears to contradict Washington's insistence that it was simply another routine freedom-of-navigation operation.

The months leading up to the patrol allowed Beijing to harden its stance and, according to some U.S. officials and security experts, blew the operation out of proportion.

Washington's caution also caused disquiet among some military officials in Japan and the Philippines, both U.S. security allies, feeding concerns that China's ambitions in the South China Sea would go unchecked.

The Pentagon and U.S. military officials had been ready for months to carry out patrols, but ran into "repeated stalling" from the White House and State Department, said one U.S. defense official, who requested anonymity.

Both wanted to avoid giving the appearance that any operation was in response to other events, the official said, such as the breach of 21 million U.S. personnel records that has been linked to hackers in China. China has denied involvement in the attack.

"The concern was that, if we looked like we were responding to something the Chinese had done, it would undermine our assertion that this is a matter of international law, and our rights to navigate the seas," said the official.

The State Department did not respond officially to queries on why the mission took so long. The White House declined official comment on the criticism.

Pressure for action was growing at a sensitive time in U.S.-China relations, as major powers moved closer to agreeing a nuclear deal with Iran and as Washington prepared for a state visit by Chinese President Xi Jinping in September.

By late September, a consensus had been reached to go ahead with the patrol, despite Xi’s assertion in Washington that China had “no intention” to militarize the islands.

Obama, who has sought to avoid confrontations with U.S. rivals and reduce direct U.S. involvement in wars, had to carefully weigh the need to take action with the risks of sparking an unintentional armed conflict that could have severe diplomatic and economic consequences.

Under his "pivot" to Asia, 60 percent of the U.S. Navy's assets will be deployed in the Pacific region by 2020, in a challenge to China's rapidly growing maritime power and ambitions.

Another U.S. official said a key reason for the lengthy internal deliberations was to be sure that every possible measure was being taken to minimize the risk of a U.S.-China military confrontation at sea. Having Obama and other senior U.S. officials publicly telegraph the likelihood of a naval patrol in the area was part of a “no surprises” strategy toward the Chinese, the official said.

A senior Obama administration official said the government had gone through a "rigorous inter-agency process" to come up with options for the president.

“Our aim was to ensure we made smart decisions to advance our strategic objectives in the Asia-Pacific region, including on maritime issues,” the official said.

NOT SO ROUTINE

Pentagon officials say the United States regularly conducts freedom-of-navigation operations around the world to challenge excessive maritime claims. China claims most of the South China Sea. Other claimants are Vietnam, the Philippines, Malaysia, Brunei and Taiwan.

Under the U.N. Convention on the Law of the Sea, 12-nautical mile limits cannot be set around man-made islands built on previously submerged reefs. Four of the seven reefs China has reclaimed over the last two years, including Subi, were submerged at high tide before construction began, legal scholars say.

Another source familiar with the matter said the administration's determination to keep the issue focused on the 12-mile territorial limits and avoid any sense the patrols were aimed at challenging Chinese sovereignty had delayed the process. While it insists on freedom of navigation through the waterway, Washington takes no position on the various sovereignty claims.

Apparently attempting to avoid further stoking Chinese anger, the White House stuck to its plan to keep its comments relatively low-key in the aftermath of the patrol, portraying it as a routine "freedom of navigation operation" that did not assert any "special specific U.S. rights".

But the hold-up subverted the initial intent to make the patrols a routine part of operating in one of the world's busiest sea lanes, through which $5 trillion in ship-borne trade passes every year, the source said.

"Delaying the patrols actually made it into a bigger deal," said the source. "This may have diminished the initial strategy that these patrols should be a regular, ordinary matter."

Bonnie Glaser a security expert at Washington's Center for Strategic and International Studies, said the mission was complicated by the fact it took so long.

"All of this attention that has been given to it has undermined the effectiveness of freedom of navigation operations," she said.

PRESSURE FROM ASIAN ALLIES

One former senior U.S. official said there had been concern within the administration, dating back to last year, that China might have drawn the "wrong lesson" from the Western response to Russia's seizure of Ukraine's Crimea region in early 2014 as well as Obama's avoidance of direct military action in Syria.

Since China's land reclamation began in December 2013, it had reclaimed more than 2,900 acres (1,170 hectares) of land as of June, the Pentagon said in a recent report. China had reclaimed 17 times more land than the other claimants combined over the past 40 years, it added.

Pressure for action from U.S. allies in the region grew after China's island-building became front-page news this year following the release of high-resolution satellite images that showed the scale of the work.

In the Philippines, civilian and military leaders publicly welcomed Tuesday's patrol.

But one Philippine military official, speaking on condition of anonymity, added: "It's about time America showed it remained engaged in this region."

Tokyo also said it supported the mission, although one commentator said there had been some scepticism in Japan over whether it would go ahead.

"I think many serious people must have been relieved to hear that the United States did what they said (they would do), unlike in similar incidents in Syria," said Kunihiko Miyake, a former Japanese diplomat.

None of America's allies in Asia have run freedom of navigation patrols past China's islands.

The U.S. administration has long been aware that patrols alone will not be enough to deter China's island-building but believed it was still important to more directly challenge China's territorial claims, a source close to the matter said ahead of the operation.

Not all experts pointed the finger at the White House and the State Department for not acting sooner.

Doug Paal, director of the Asia Program at the Carnegie Endowment for International Peace, said he believed the U.S. Navy had been internally conflicted for a few years over whether to go ahead with the patrol.

"Now both Beijing and Washington have to show their people they are tough and will not be pushed around, without actually triggering an entirely purposeless conflict," added Paal.

A senior Navy official denied there had been any internal Navy tension over the patrol, adding that such decisions had to be made by the defense secretary and the president.

(Additional reporting by Phil Stewart in Washington; Linda Sieg, Tim Kelly and Nobuhiro Kubo in Tokyo and Manuel Mogato in Manila. Writing by Dean Yates; editing by Stuart Grudgings.)