If Japan’s earthquake, tsunami and nuclear crisis are any indication, what they say is true: Sometimes what can go wrong will go wrong. And when it comes to operating nuclear plants, what are some of the risks? Here’s a brief guide, drawing from what we’ve learned in recent days:

Weaknesses in reactor design

One concern surrounding the safety of nuclear plants is the potential weakness in certain kinds of protective devices.

While nuclear reactors like the one in Japan are designed to shut down when an emergency occurs, nuclear fuel still needs to be adequately cooled to prevent radioactive material from melting through protective barriers and escaping into the environment. The Fukushima Daiichi plant uses a type of reactor called a “boiling water reactor.”

GE is the designer of such reactors in the U.S., which use protective barriers known as “containment units” to keep radioactive material from leaking into the environment should the cooling systems fail. Other reactor types have containment units, too, but GE’s use what’s called a “pressure-suppression” design, which is smaller and cheaper to build than the larger, concrete-reinforced containments.

These containment units, also designed by GE, come in three models – “Mark I,” and the more recent “Mark II” and “Mark III.”  According to the NRC, 35 of the 104 nuclear plants in the U.S. use boiling water cooling systems; 23 still use Mark I containment units like the one in Fukushima, and 12 reactors use the later Mark II or Mark III units.

According to the New York Times, safety officials have expressed concerns about ”pressure-suppression” containment units for decades, claiming they might be “physically less robust” and “more susceptible to failure in an emergency” than other types of containment units.

McClatchy Newspapers reported today that in 1976, three GE engineers resigned over concerns that the Mark I containment systems were not strong enough to contain the steam pressure that would build up if the reactor’s cooling system failed.

On Wednesday, GE also told the Wall Street Journal that it made changes to Mark I designs in the U.S. “after tests of Mark III designs exposed weaknesses common to all the structures,” but that it was “still trying to determine” if similar, suggested changes were made in Japanese units. GE has also defended the designs, pointing out that even the older Mark I units have “a proven track record of safety” and that “there has never been a breach of a Mark 1 containment system.”

As the Times reported today, one reactor’s containment system may have been breached. Workers at the Daiichi plant have been venting radioactive steam from the other reactors to avoid further breaches.

Failure of backup mechanisms

While containment units are typically the last line of defense, several other backup systems are supposed safely cool the nuclear reactor and prevent a meltdown in the first place.

When a boiling water reactor loses electrical power, it will switch to diesel-powered backup generators to pump in water and cool the reactor. If the back-up generators fail, the plant may switch to emergency batteries. In case of a total power failure, power plants must find other ways to truck in water and prevent the reactor from overheating.

In Japan, officials have had to pump in seawater, but other reactor designs – like the more common pressurized water reactors -- can use natural forces like gravity to drain water into the reactor from nearby reservoirs.

Limited Audits by Regulators and Little Accountability for Owners

While the odds of a nuclear plant disaster are low and even the most severe nuclear accident in U.S. history—the 1979 accident at Three Mile Island—resulted in no fatalities, a report yesterday by the Union of Concerned Scientists noted 14 “near misses” at U.S. nuclear plants in 2010.

According to the report, the “near misses” occurred because “reactor owners, and often the NRC, tolerated known safety problems.” It noted that regulatory audits of reactors are limited, so most problems are left to reactor owners to address, which doesn’t always happen:

The NRC cannot be blamed for safety problems in areas it does not examine, but the agency deserves considerable blame for failing to correct safety problems it has identified. When the agency’s limited-scope audits find broken devices, the failures of the plants’ testing and inspection regimes to find and fix these devices are the true safety problems. By failing to insist that owners correct these true safety problems, the NRC does nothing about the 90–95 percent of conditions and activities in nuclear plants that it does not audit.

The report’s author, David Lochbaum, is a former NRC safety instructor. A NRC spokesman told the Times, “We think our oversight is good and a corporate culture of safety is important to us.”

President Obama, seeking to allay fears sparked by Japan’s nuclear crisis, ordered the NRC to review the safety of U.S. nuclear plants, though he said U.S. plants have “undergone exhaustive study and have been declared safe for any number of extreme contingencies.”

The Associated Press reported today that in Japan, a cozy relationship between government regulators and the energy industry resulted in problems being overlooked.

Dangers of nuclear waste

As we’re learning from Japan, byproducts from nuclear plants can also pose risks.

”Spent fuel rods,” for instance, are radioactive byproducts of the process used to generate energy at nuclear plants. In Japan, their dangers appear to currently outweigh those posed by the reactors themselves.

The fuel rods are stored for years in water ponds while their radioactivity drops. The purpose of this is twofold: the water cools the rods and provides radiation shielding. In 2005, a Government Accountability Report found that federal regulators in the U.S. had failed to properly oversee the handling of this radioactive waste.

Last year, the Associated Press reported that 27 of the country’s 104 nuclear reactors were leaking low-levels of radioactive tritium into groundwater.

A patchwork of emergency response plans

Individual nuclear plants and government agencies are required to maintain detailed response plans to handle emergency situations including the threat of a nuclear crisis. The Nuclear Regulatory Commission has the statutory authority to manage incidents at nuclear plants, but critics have questioned whether the roles of federal and state agencies are sufficiently laid out.

According to the White House and NRC, the level of federal response to any given radiological emergency would depend on the nature of the incident.

Some states also have drawn up their own contingency plans for a nuclear emergency, including the stockpiling of potassium iodine tablets. These tablets, as we’ve noted, help limit the absorption of a particularly harmful radioactive material—radioactive iodine—but their effectiveness is limited.