Qantas has confirmed it found a structural crack in a third aircraft during an inspection of its Boeing 737 fleet.

"Of the 33 of Qantas' 737 aircraft that required inspection, three were found to have a hairline crack in the 'pickle fork' structure. These aircraft have been removed from service for repair," a statement from the airline read.

Qantas head of engineering Chris Snook and Qantas Domestic chief executive Andrew David say the affected plans will be back in the air by the end of the year. Louise Kennerley

The "pickle fork" structure attaches the wing to the plane's body. The cracks in all three aircraft are "touching the same spot, adjacent to the same bolt", Qantas head of engineering Chris Snook said on Friday.

The aircraft removed from service had all completed about 27,000 flights. Any aircraft with more than 22,600 flights was inspected, in line with advice from regulators.

It leaves the airline short of domestic aircraft for several weeks as it waits for Boeing to repair the cracks on the planes, which make up the backbone of its short-haul operations.

The cracks - which Qantas said did not immediately compromise safety - are a worldwide issue affecting Boeing's popular 737 NG model aircraft.

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Qantas brought forward the precautionary checks by up to seven months, completing them in seven days, the statement said.

"Qantas will minimise any customer impact from having these aircraft temporarily out of service," it said.

"Qantas is working with Civil Aviation Safety Authority and Boeing to resolve this issue, which involves some complex repair work."

The airline discovered the cracks in the first aircraft during routine maintenance in Brisbane in the past few days and grounded the plane for repairs.

There are calls to ground all of Qantas’s Boeing 737’s due to faults found near the wings of at least one of the aircrafts.

The Australian Licensed Aircraft Engineers Association said on Thursday morning that a crack in a second aircraft's primary wing structure was discovered overnight, and called for the grounding of all 75 of Qantas' 737 aircraft.

Qantas Domestic chief executive Andrew David said on Friday: "As people would expect with Qantas, we've gone above what was required to check our aircraft well ahead of schedule.

"Let me be very, very clear on that point. Qantas will never fly a plane if we do not believe it is safe to do so. Our entire reputation, our brand, is built on a safety record," he said.

Mr David said the repair process was "complex" and was it expected to "take through to the end of the calendar year to get those three aircraft flying again".

He added that, despite the cracks in the 737NG fleet and the ban on Boeing 737 MAX aircraft from flying following two crashes, Qantas still had "every confidence in Boeing".

Mr David also addressed the ALAEA's call for the airline to ground the entire 737NG fleet after the cracks were found in the second aircraft.

"Unfortunately, there were some irresponsible comments from one engineering union yesterday, which completely misrepresented the facts. Those comments were especially disappointing, given the fantastic job our engineers have done to inspect these aircraft well ahead of schedule, and the priority they give to safety every day of the week," Mr David said.

The ALAEA's federal secretary Steve Purvinas was unrepentant on Friday, and questioned Qantas' claim that the cracks did not present an immediate safety risk.

"Why then, when you find these cracks on a plane, you're not allowed to fly them?" he said.

Mr Purvinas said it was only a matter of time before aviation safety regulators ordered all planes to be checked for cracks, including the 42 Qantas 737s that are under the threshold of 22,600 flights.

"But if they're so concerned about safety, it takes one hour. Why wait, why not check the planes now?" he said.

"It's because if they find another they'll have to take it out of service."

Virgin Australia has checked 19 aircraft in its fleet that were above the 22,600 flight threshold - including four that were over 30,000 and had to be checked within a week of the US Federal Aviation Authority's directive in early October – and found no cracks.

Mr Purvinas said he was not as concerned about the rest of Virgin's 737s because it had also run precautionary checks on six additional jets above 18,000 flights. Virgin confirmed it had completed these additional checks.

In a statement, Boeing said it hoped to have the affected planes back in the air soon.

"Boeing is actively working with customers that have airplanes in their fleets with inspection findings to develop a repair plan, and to provide parts and technical support as necessary," the company said.

"Just over 1000 airplanes globally have reached the inspection threshold, with less than five per cent having findings that will need repair.

"Boeing regrets the impact this issue is having on our 737NG customers worldwide and we are working around the clock to provide the support needed to return all airplanes to service as soon as possible."

On October 2, the FAA ordered inspections within seven days of all 737 NGs that had operated more than 30,000 flights.

The FAA said that the cracks, if not addressed, "could adversely affect the structural integrity of the airplane and result in loss of control".