Mike Mount
CNN Senior Pentagon Producer

Thousands of confidential files on the U.S. military's most technologically advanced fighter aircraft have been compromised by unknown computer hackers over the past two years, according to senior defense officials.

The Internet intruders were able to gain access to data related to the design and electronics systems of the aircraft through computers of Pentagon contractors in charge of designing and building the aircraft, according to the officials, who did not want to be identified because of the sensitivity of the issue.

In addition to the intrusion into files of the Joint Strike Fighter, hackers also gained entry into the Air Force's air traffic control systems, according to the officials.

Once broken into, the internet hackers were able to see such information as locations of U.S. military aircraft in flight.

The Joint Striker Fighter plane is the military's new F-35 "Lightning II," also known as the Joint Strike Fighter, it will be the future aircraft used by all of the branches of service.

Most of the files broken into focused on the design and performance statistics of the fighter, as well as its electronic systems, officials said. The information could be used to make the plane easier to fight or defend against.

Additionally, the system used by the aircraft to conduct self diagnostics during flight was also compromised by the computer intrusions, according to the officials who insisted none of the information taken was highly sensitive data.

The plane uses stealth and other highly sensitive electronic equipment to defend itself and fight, but it does not appear that information was compromised because that information is stored on computers that are not connected to the Internet, according to the defense officials.

The Joint Strike Fighter's main contractor is Lockheed Martin Corp. while Northrop Grumman Corp. and BAE Systems PLC are major subcontractors in the planes production.

On a conference call with investors on Tuesday, a Lockheed Martin's chief financial officer denied there was any breach of classified information, which was first reported by the Wall Street Journal on Tuesday.

"The US govt doesn't talk a whole lot about this and neither do we. But in response to the WSJ report, we think it's incorrect," Bruce Tanner, Lockheed Martin's CFO, said. "There's never been any effective attack. We have measures in place and there's never been a successful attack."

In a statement released later, the company reiterated its position that no classified information had been accessed.

"To our knowledge, there has never been any classified information breech. Like the government, we have attacks on our systems continually and have stringent measures in place to detect and stop attacks," the statement said.

BAE Systems and Northrop Grumman spokespeople would not comment on the story and refered all questions to Lockheed Martin.

While the Joint Strike Fighter will have different variants for the different branches of service it will be used in, it also has many international partners helping build the plane and will be sold to U.S. allied countries.

The multiple nations involved raises concern about the level of computer security measures the partner countries have, officials told CNN.

Companies contracting with the Department of Defense now have to prove they are using the proper computer security before a contract can be awarded, Pentagon officials said. A measure put into place within the past year because of the increase in cyber intrusions, they said.

When asked if sensitive technology for the Joint Strike Fighter had been jeopardized, Pentagon spokesman Bryan Whitman said, "I am not aware of any specific concerns."

Whitman would not confirm the cyber security breach for on the Joint Strike Fighter program, but said the number of attempted attacks on the US military's network were on the rise.

"We have seen the number of intrusion attempts more than double recently," Whitman said, but he would not reveal a timeline.

Whitman said the computer systems of the Department of defense are scanned thousands of times a day by entities looking for ways inside U.S. military computer networks.

Officials could not say who was behind the computer hacking, which has occurred numerous times since 2007. The intruders were able to cover their tracks making it look like the virtual break-ins were coming from various parts of the world, according to officials. The Wall Street Journal reported that the attacks appeared to orginate in China, citing "former U.S. officials."

Last month a Pentagon annual report to Congress about China's military power said China has been making continued progress in developing cyber warfare techniques.

The report noted that U.S. government computers were the target of "intrusions that appear to have originated" from China, although they were not confirmed to be from the Chinese military.

CNN requested a comment about the accusation from the Chinese Embassy in Washington. An embassy spokesman denied the allegations to the WSJ.

The Air Force, the main program manager of the JSF program, has a number of ongoing investigations into the multiple hackings, officials said.

The officials said a number of safeguards have since been put into place to protect that system.

– Producer Eric Marrapodi contributed to this report