It was not immediately clear how much damage the water may have caused, and searchers could not definitively say what was inside the crate.
But British aviation enthusiast David J. Cundall, who is driving the hunt for the rare Spitfire planes, called the results "very encouraging."
"It will take some time to pump the water out ... but I do expect all aircraft to be in very good condition," Cundall told reporters in Myanmar's main city, Yangon.
The single-seater Spitfire, which helped Britain beat back waves of German bombers during the war more than six decades ago, remains the most famous British combat aircraft.
Britain built a total of about 20,000 Spitfires, although the dawn of the jet age meant the propeller-driven planes quickly became obsolete.
As many as 140 Spitfires — three to four times the number of airworthy models known to exist — are believed to have been buried in near-pristine condition in Myanmar by American engineers as the war drew to a close.
The wooden crate located in northern Myanmar was found in Myitkyina in Kachin state during a dig that began last month. It is one of several digs planned nationwide, including another near the airport in Yangon.
Cundall said the search team in Kachin state inserted a camera into the crate and found it was full of water. It was unclear what was inside the crate, he said, but the water will be pumped out during an operation that could take weeks, he said.
The go-ahead for excavation came in October when Myanmar's government signed an agreement with Cundall and his local partner.
Under the deal, Myanmar's government will get one plane for display at a museum, as well as half of the remaining total. DJC, a private company headed by Cundall, will get 30 percent of the total and the Myanmar partner company Shwe Taung Paw, headed by Htoo Htoo Zaw, will get 20 percent.
During the project's first phase, searchers hope to recover 60 planes: 36 planes in Mingaladon, near Yangon's international airport; six in Meikthila in central Myanmar; and 18 in Myitkyina. Others are to be recovered in a second phase.
Searchers hope the aircraft are in pristine condition, but others have said it's possible all they might find is a mass of corroded metal and rusty aircraft parts.
Cundall said the practice of burying aircraft, tanks and jeeps was common after the war.
"Basically nobody had got any orders to take these airplanes back to (the) UK. They were just surplus ... (and) one way of disposing them was to bury them," Cundall said. "The war was over, everybody wanted to go home, nobody wanted anything, so you just buried it and went home. That was it."
Stanley Coombe, a 91-year-old war veteran from Britain who says he witnessed the aircraft's burial, traveled to Myanmar to observe the search.
It is "very exciting for me because I never thought I would be allowed to come back and see where Spitfires have been buried," Coombe said. "It's been a long time since anybody believed what I said until David Cundall came along."
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