Saturday’s crash of Lion Air Flight 904 in the resort island of Bali is unlikely to help the Jakarta, Indonesia-based airline in its fight to be removed from a European Union safety blacklist, nor is it good news for a brand that’s just purchased record volumes of Airbus and Boeing jets.

Indonesian investigators began their probe Sunday into how a new Boeing 737-800 passenger jet missed a runway and skidded into shallow waters near the Ngurah Rai International Airport in Denpasar, Bali.

Although the plane crashed into the sea and snapped in half, none of the 108 passengers and crew members aboard was killed.

The National Transportation Safety Committee removed the plane’s flight-data recorder Sunday and planned to tow the aircraft onto a beach at high tide. Meanwhile, divers were looking for the cockpit voice recorder, according to local media reports.

Initial debriefings, weather reports and witness comments assert that wind shear may have played a role in the accident. The flight originated in Bandung, the capital of West Java province, and encountered stormy skies in the approach to Bali.

Others believe pilot error was to blame for the plane belly-flopping into the sea. Whatever the reason, the accident once again cast a spotlight on Indonesia’s less-than-stellar aviation record and its largest private carrier.

Lion Air, which began service in 2000, gave Boeing its largest-ever order last year when it inked a deal for 230 planes. Just last month, the discount carrier signed a deal to buy 234 Airbus planes, also that company’s largest order to date.

Some $45 billion later, Lion Air has 559 narrow-body planes pending, more than any other global carrier.

Moving forward, Edward Sirait, the commercial director of Lion Air, said in an April 1 interview with Indonesia’s TVOne, that the company was considering partnerships in Myanmar, Thailand and Vietnam with hopes of having 1,000 planes in 10 years.

Lion Air already has a 45 percent market share in Indonesia, a sprawling nation of more than 240 million people that has seen a boom in both economic growth and air travel. Amid its rapid expansion, however, several issues have been unearthed.

Five Lion Air pilots were arrested during the past two years for drugs, according to local media reports, raising questions of whether drug abuse or overwork are widespread on the carrier.

Lion Air has also been involved in six accidents since 2002, four of which involved Boeing 737s and one of which resulted in 25 deaths, according to the Aviation Safety Network.

The carrier was banned from flying to Europe in 2007 due to broader safety concerns in the Indonesian airline industry. Although the EU lifted the ban on many other Indonesian carriers in 2009, Lion Air remains blocked -- a penalty it has called unfair.

Indonesia is one of the fastest-growing markets for airlines, but it has struggled to staff its planes with qualified pilots and service them with trained mechanics. Further troubles with air traffic control and outdated airport technology remain of concern.

“With over 18,000 islands crossing an expanse of over 5,000 km, aviation is the critical link,” International Air Transport Association Director General and CEO Tony Tyler explained in a report on Indonesia’s safety and infrastructure challenges. “Only aviation can connect efficiently Indonesia’s nearly 240 million inhabitants domestically and to the world. So it is important that the government has coordinated policy measures, including the critical issues of ensuring safety and adequate infrastructure for development.”

Tyler claimed that Indonesia is projected to be the sixth-fastest-growing market for international passengers and will likely have the ninth-largest domestic market by 2014.

“Alongside its significant domestic traffic, its location at the heart of southeast Asia gives this market tremendous potential,” he noted. “As the Association of Southeast Asian Nations moves forward with liberalization, it is important that Indonesia is well-prepared with a safe industry operating on global standard infrastructure.”

Indonesia accounts for 1.4 percent of global traffic, but 4 percent of all accidents, IATA pointed out in its report. Three out of four incidents were runway mishaps.