JAKARTA--The pilot and co-pilot of the Lion Air passenger plane that crashed at Bali's airport passed their initial drug tests, authorities said Sunday, as investigators continued their search for the accident's cause.

While initial urine tests showed no signs the pilots were using drugs, authorities said they were also analyzing hair, which can be more conclusive. Such tests are standard procedure after accidents.

The new Boeing Co. (BA) aircraft missed the runway at the resort island's airport Saturday and crashed into shallow water.

The aircraft broke in two, but all the 108 passengers and crew survived. Dozens were injured, but most had been released from the hospital by Sunday. Among those with slight injuries were the flight's three foreign passengers, two Singaporeans and one French national.

Lion Air and transportation authorities said it was too early to determine the reason for the crash. But investigators are bound to examine, among other factors, whether a sudden wind shift or some onboard problem shortly before the jet's planned touchdown, when its altitude was only a few hundred feet above the water, caused the accident. Preliminary indications are that the approach was normal until perhaps the last minute or two of the flight, according to safety experts who have reviewed publicly available data.

These experts also said that barring reduced visibility from a suddenly intense burst of rain, the pilots should have been able to use visual references and navigation aids at the airport to judge their approach and to realize they were descending too quickly.

Saturday's crash was unusual because running off the end of a runway, often after landing too fast and too far down the strip, continues to be the most common type of commercial aircraft accident world-wide. By contrast, touching down before reaching a runway--called undershooting the approach--isn't considered a major safety hazard for airliners. Safety experts pointed to only a handful of serious accidents since 2005, all involving regional airliners with fewer seats that the Lion Air jet, prompted by pilots landing short of a runway.

The Indonesian airline has had five incidents in the past 11 years, analysts said, several of which involved its planes having trouble landing. In the worst accident, in 2004, one of its flights overshot a runway in Solo in central Java, killing more than 25 passengers.

Indonesian President Susilo Bambang Yudhoyono said Sunday that he had ordered an investigation into Saturday's crash. "I have instructed the transportation minister to take care of those who were injured and launch an investigation," he said.

Television reports through the weekend showed the cracked fuselage of Lion Air's new Boeing 737-800 in the waves as well as passengers wrapped in blankets being rolled on stretchers into nearby hospitals.

Eyewitnesses said the plane, which was flying through heavy rain, seemed to be trying to land and crashed short of the runway. The Ngurah Rai Airport is one of the busiest in Indonesia: It is the main gateway to the more than two million international tourists who arrive in Bali every year and is in the middle of major expansion construction.

"Both the plane and the pilot were fit to fly," Lion Air director and spokesman Edward Sirait said at a news conference Saturday. "The plane was delivered in late March."

Five Lion Air pilots have been arrested for alleged illegal drug use in the past two years. But the initial tests suggest that isn't the case in this accident.

"We have conducted tests on them on Saturday, with the urine test showing negative results," said Bambang S. Ervan, spokesman for the Indonesian Public Transportation Ministry from Ngurah Rai Airport.

A Boeing spokeswoman in Singapore declined to be interviewed but said the company is "standing by to assist as needed."

Indonesia's Director General of Civil Aviation, Herry Bakti, told reporters the aircraft was scheduled to be lifted from the water Sunday. It will be kept in a safe place for further investigation. Mr. Bakti said one of the black boxes from the plane was retrieved Saturday.

Lion Air in recent months has placed orders for hundreds of new aircraft as the airline seeks to become one of the world's largest by serving the growing middle class in Indonesia and the rest of Southeast Asia.

Airbus, a unit of European Aeronautic Defence & Space Co. (EADSY, EAD.FR), reached a deal in March to supply Lion Air with 234 jetliners. Lion Air placed a similar large order with Boeing last year.

While Lion Air and other airlines have big plans for Indonesia, the country's air-safety standards and regulatory system have sparked international concern following a spate of deadly accidents over the past decade.

The U.S. in 2007 downgraded Indonesia to the lower of two safety classifications. The European Union soon after placed the country on its list of countries and carriers unsafe for flying.

Lion Air and most Indonesian carriers are on the list because their country is, and not necessarily because of safety issues at the airlines.

Boeing, Airbus and air-safety experts from around the world have worked with Indonesia to improve its aviation-safety standards.

The number of fatal accidents in Indonesia has fallen over the past two years, but the country hasn't improved regulation sufficiently to be upgraded. The EU in December noted "sound progress' but said Indonesian authorities must "continue efforts toward completing their work of establishing an aviation system fully compliant" with United Nations standards.

Whether the accident might hurt Lion Air's ambitious expansion plans is unclear.

"They have a lot of big ambition, so they will have to see," said Siva Govindasamy, Asia managing editor for Flight Global, an aviation-industry publication. "They have actually really improved [the company's image] over the last couple of years. They are trying to show they are a serious player in the airline industry."

One government official said that no airline will be allowed to expand rapidly unless it can prove that it can build in all the necessary safety measures as it grows.

"We evaluated all of [Lion Air's] expansion," said the Transport Ministry's Mr. Bakti. "We control its expansion, so as it doesn't compromise safety."

-- Andy Pasztor in Los Angeles contributed to this article.

Write to Eric Bellman at eric.bellman@wsj.com and I Made Sentana at i-made.sentana@dowjones.com

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