The government watchdog reports issued this month on the $400 billion F-35 Joint Strike Fighter join a long list of critical reviews that have picked apart the program’s ballooning cost, schedule delays, problems with software and even the helmet.

Now the Government Accountability Office and the Pentagon’s internal investigator have taken aim at the engine of the most expensive weapons system in the history of the Pentagon.

In a report issued earlier this month, the GAO, using unusually strong language, said that the “reliability of the engine is very poor” and that “the program has a long way to go to achieve” reliability goals.

Then, in a report released Monday, the Pentagon’s internal investigators said there were 61 violations in how the engine program is being managed — dinging Pratt & Whitney, the engine manufacturer, for a variety of missteps, including workers not always wearing protective gloves and masks when working around dangerous materials and assembly areas not cleared of foreign objects that could cause damage to the engines.

It is not the first time the watchdogs have found flaws in the program — the GAO lists 40 related reports that date back a decade on the F-35. And it is certainly not the last time the controversial fighter jet will face scrutiny and criticism.

But now the Pentagon and the companies involved in the program are pushing back.

Pratt & Whitney scheduled a news conference that came about an hour after the Pentagon inspector general’s report was released, to defend the program and offer context it says the investigators missed. Bennett Croswell, president of military engines for Pratt, was quick to point out that the report was an audit of the company’s management systems and adherence to the contract.

The report “does not speak to the quality of our products, which we believe are world-class,” he said. “The engine is reliable.”

The Pentagon office that oversees the F-35 disagreed with three of the inspector general’s six findings. It said that the recommendations for corrections “are unnecessary, and, if implemented, would add cost and schedule growth to the program for items that are already well understood and carefully managed.”

The aggressive stance follows a forceful defense of the program last month by Air Force Lt. Gen. Chris Bogdan, who said that costs are coming down, key milestones are being met and many of the issues that drove up the program’s cost have been remedied.

It is a critical time for the F-35, which is built by Bethesda-based Lockheed Martin and is often derided by critics as the “jet that ate the Pentagon.” A July 1 deadline is looming for the Marine Corps version of the plane to reach what is called “initial operational capability,” when it would be declared ready for combat.

Pentagon officials concede that the program was way over budget and years behind schedule. But in recent years, under new leadership, it has gotten back on track, they say.

Still, in its report, the GAO found that “improving engine reliability will likely require additional design changes and retrofits” that could require even more money and time.

To rebut that, Croswell came to the news conference armed with charts and data on the engine’s performance, and pointed out that the F-35 recently performed very well, taking off and landing on a carrier last fall. The company plans for the engine to last as much as 50 percent longer than required.

Asked if he was surprised by the GAO’s conclusion that the engine was unreliable, he said, “Yes, very much so.”

The entire fleet of F-35s was grounded last summer after an engine fire during a training mission at Eglin Air Force Base in Florida as a pilot was beginning to take off. The root cause of the problem has been discovered and fixed, officials said. And problems in a development program are to be expected, they said.

But as the GAO noted, the fact that the aircraft is in development at the same time it is being manufactured has caused problems, which critics have long said was a violation of the acquisition tenet “Fly before you buy.”

Another problem is that the F-35 is going to have to compete “with other large programs for limited acquisition resources,” putting pressure on the budget at a time when defense spending is being trimmed.

And the GAO predicted that, given the complexities of the program, the literature of criticism is only going to grow.

“With more complex and demanding testing ahead and engine reliability improvements needed, it is almost certain that the program will encounter more discoveries,” the report said.