For the second time in less than two years, a mid-air rupture in the roof of a Southwest Airlines jet has sparked questions about the safety of its fleet.

The Boeing 737-300 was cruising at 36,000 feet last week when a hole burst in the ceiling, creating passenger pandemonium in the fast-depressurizing cabin and forcing the pilot to make an emergency landing in Yuma, Ariz.

If all this sounds uncomfortably familiar, it’s because in July 2009, another Southwest 737-300 had to make an unexpected landing after a football-sized hole ripped open in its roof.

One incident is troubling; two raises all sorts of red flags. Yes, Southwest has been quick to show it’s putting safety first, grounding scores of planes and canceling hundreds of flights for special inspections since the latest frightening episode. Much more needs to be done — by the airline, Boeing and the Federal Aviation Administration, to understand what happened this time and how to prevent another.

All planes develop tiny cracks in their skins as they age, flaws that usually don’t turn into something worse despite repeated landings and takeoffs. Most cracks are found and repaired during routine maintenance. But sometimes these inspections overlook cracks, and when fault lines intersect, the risk of mid-air crisis increases.

Further complicating the picture is that, depending on a jet’s operator, purpose and even location, a single type of aircraft can be flown and maintained in many different ways. All of that must be taken into account as regulators examine whether safety inspections have been adequate.

This much is certain: Passengers who found themselves gazing in horror at the sky during the Phoenix-to-Sacramento flight probably would steer clear of the word “adequate” right now.

Investigators should focus on the age of the aircraft, the stress of repeated takeoffs and landings, safety inspection mistakes and even structural design issues. The 737-300 accounts for about a third of Southwest’s fleet; its youngest such jet is 13 years old, slightly newer than the average age of fleets at other major carriers.

The FAA late Monday issued an emergency directive calling for increased structural inspections on older models of the 737. If structural problems related to design, stress or age are found to be greater than the industry average, regulators should consider permanently grounding this particular aircraft. And if Southwest cut corners or conducted shoddy inspections, the airline should face stiff fines and other penalties.

As recently as 2008, the FAA fined Southwest $10.2 million for knowingly flying 46 jets that were overdue for fuselage inspections. Southwest eventually paid a reduced fine of $7.5 million and changed its maintenance manuals.

Southwest has built a well-deserved reputation for low-cost, efficient and competitive service. It must now draw on that history.

Similarly, the airline industry takes pride in noting that its jets undergo rigorous inspections and literally are taken apart piece by piece and reassembled during heavy maintenance.

If that’s the case at Southwest, these busted-out roofs are even more of a mystery that demands fresh answers.