Within months of the National Security Agency document leaks by Edward Snowden, al-Qaida and its affiliates had made changes based on the information revealed, according to RT.

The NSA had repeatedly said this would occur and that Snowden's actions could harm the safety of the U.S. and its troops, but no hard data had been used to support the claims previously.

That has changed as a report from a Massachusetts company has found three separate incidents following the whistleblower's actions that indicated there was indeed a negative effect from the leaks.

"This is as close to proof that you can get that these have changed and improved their communications structure post the Snowden leaks," Recorded Future's CEO and co-founder Christopher Ahlberg told NPR.

Recorded Future worked with Reversing Labs, a file analysis and software protection company, both in Massachusetts, to seek out the data. What they uncovered was a change in the software used by al-Qaida, which had not been altered since it rolled out in 2007, according to NPR.

The first report from the duo, in May, revealed some of the changes.

"The prior research focused on a single point: Following the June 2013 Edward Snowden leaks we observe an increased pace of innovation, specifically new competing jihadist platforms and three major new encryption tools from three different organizations -- GIMF, Al-Fajr Technical Committee and ISIS -- within a three to five-month time frame of the leaks," according to Recorded Future.

GIMF and Al-Fajr prefer Androids for their mobile use and those platforms saw changes as well soon after the initial report by Recorded Future.

But Bruce Schneier, of Harvard's Berkman Center, told NPR, "Certainly they have made changes, but is that because of the normal costs of software development or because they thought rightly or wrongly that they were being targeted?"

Schneier said that whatever the reason, it is still possible for NSA to spy on them because all software has vulnerabilities.

"It is relatively easy to find vulnerabilities in software," he said. "This is why cybercriminals do so well stealing our credit cards. And it is also going to be why intelligence agencies are going to be able to break whatever software these al-Qaida operatives are using."