Only three commercial flights among the thousands that operated nationwide in June sat on the ground loaded with passengers for three hours or longer, the Obama administration said Tuesday, touting the effect of a controversial new consumer-protection rule that threatens stiff fines against airlines for excessive tarmac delays.

The bad news for Chicago was that all three overly tardy flights involved the home-town carrier, United Airlines, at O’Hare International Airport.The situation that played out in an early summer day of severe thunderstorms at O’Hare demonstrates how the rule that took effect in the spring forces airlines to tightly balance their first priority — delivering passengers safely to their scheduled destinations — against the need to avoid time-limit violations and the punishing fines that could accompany them.

But on a national scale, the trio of United flights stranded for as long as three hours and five minutes amid heavy rains at O’Hare  June 18 marked a dramatic reduction in long tarmac delays from the same month last year, according to the U.S. Department of Transportation. Some 268 flights nationwide were delayed at airports for at least three hours in June 2009, according to the department’s Air Travel Consumer Report.

There was no increase in the rate of canceled flights this June, either, officials said, explaining that airlines canceled 1.5 percent of their scheduled domestic flights both in June and June a year ago. Some aviation experts had predicted that faced with the possibility of multi-million-dollar fines for every seriously delayed plane, airlines would implement wholesale cancellations in poor weather well before the three-hour tarmac limit, inconveniencing the flying public more deeply than by waiting out long flight delays and eventually taking off.

The government’s June data on cancellations contrast with a George Washington University study based on preliminary data from May showing that canceled flights soared more than 40 percent since the new rule took effect on April 29.

Still, some airline industry experts reject the government’s interpretation of the data and its contention that the new tarmac rule is serving the public well.

“The DOT can beat its chest all it wants about how it is taking care of the consumer, but the drop in lengthy delays is because the airlines are scheduling differently and canceling and diverting more flights,” said Michael Boyd, an aviation analyst based in Colorado. “You cannot compare this year and last year because the weather is different, airline scheduling is different and passenger demand is changing.”

The tarmac rule provides for fines of up to $27,500 per passenger against airlines that idle planes on airfields for more than three hours without offering to let passengers exit, except in situations where safety would be compromised. Food and drinks must be provided once a ground delay lasts for two hours.

One of the three United planes waiting out the storm on June 18 at O’Hare eventually departed after a three-hour and two-minute delay, said United spokeswoman Megan McCarthy. The other two flights returned to the gate and were canceled, she said, adding that passengers had to wait until the next day to depart.

Due to extensive taxiing times across the crowded O’Hare airfield back to the gate, the two canceled flights recorded delays of three hours and three minutes and three hours and five minutes, respectively, McCarthy said.

“We could have started returning to the gate earlier, but departure was imminent,” she said, adding that by returning to the gate the planes lost their place in the departure queue and the two flights were canceled. “Our focus is to always get our customers to their destinations if at all possible,” McCarthy said.

“The weather on June 18 caused severe air-traffic control delays at O’Hare and a few times prevented our employees from safely loading and unloading aircraft in a timely manner,” she said, adding that compensation was offered to customers on the canceled flights.

The government has not assessed penalties against United so far for the three violations of the rule in June or for four violations incurred by United in May during a snowstorm in Colorado, McCarthy said.

June, overall, was a bad month in terms of on-time performance for O’Hare and United. O’Hare placed 28th for on-time departures, and dead last for on-time arrivals, among the 29-busiest U.S. airports, according to the U.S. Bureau of Transportation Statistics.

United ranked No. 8 among the top-18 airlines in June for on-time arrivals. Seventy-nine percent of United flights systemwide arrived on time in June. United fared better for the first six months of 2010, with an 83 percent on-time arrival rate, good enough to take the No. 3 spot among carriers.