While the State Department’s own internal probe found former Secretary Hillary Clinton violated federal recordkeeping laws, it’s not the first time she and her top aides shielded her email from public disclosure while serving in a government position.

As first lady, Hillary was embroiled in another scheme to bury sensitive White House emails, known internally as “Project X.”

In 1999, as investigators looked into Whitewater, Travelgate, Filegate and other scandals involving the then-first lady, it was discovered that more than 1 million subpoenaed emails were mysteriously “lost” due to a “glitch” in a West Wing computer server.

The massive hole in White House archives covered a critical two-year period — 1996 to 1998 — when Republicans and special prosecutor Ken Starr were subpoenaing White House emails.

Despite separate congressional investigations and a federal lawsuit over Project X, high-level emails dealing with several scandals were never turned over. And the full scope of Bill and Hillary Clinton’s culpability in the parade of scandals was never known.

To those well-versed in Clinton shenanigans, this all sounds distressingly familiar.

Thanks to another server-related problem, Clinton so far has gotten away with withholding more than 30,000 emails from congressional committees investigating the Benghazi terrorism cover-up, Clinton Foundation foreign-influence peddling and other scandals.

“This Clinton email scandal is nothing new,” Judicial Watch president Tom Fitton told me. “There were previous efforts to hide emails in the Clinton White House.”

His Washington watchdog group filed a lawsuit to recover the missing White House emails back then, just as it has against the State Department now, though it has had better luck in this case.

The parallels don’t end there.

During the Project X email scandal, career White House staffers and contractors found that someone close to the first lady had basically turned off the White House’s automated email archiving system. They fingered White House “special assistant” Laura Crabtree Callahan, who was overseeing the computer contractors despite obtaining computer science degrees from diploma mills.

The State Department staffer who set up Clinton’s unsecured server in the basement of Clinton’s home in Chappaqua also lacked computer experience and qualifications.

Clinton so far has gotten away with withholding more than 30,000 emails from congressional committees investigating the Benghazi terrorism cover-up, Clinton Foundation foreign-influence peddling and other scandals.

That IT staffer, Bryan Pagliano, appears to be playing a similar role in this email caper as Callahan did in the White House — that of a lackey used to help thwart public requests to see information about the government-related business of the Clintons.

Despite having no computer security experience or even security clearance, Pagliano catapulted from a Clinton campaign worker to the secretary’s own “special adviser” dealing with the department’s classified email system.

On top of his $133,000-a-year State Department salary, Clinton personally paid Pagliano thousands of dollars between 2009 and 2013 to set up and run a private home-brew server for her, separate from the government system she was supposed to use, where she received and stored thousands of classified government emails. His work for the secretary was clearly a rogue operation, because the department’s inspector general found that his boss, the deputy chief information officer, was “unaware of his technical support of the secretary’s email system.”

Like Callahan before him, Pagliano had unusual access to Clinton. The one qualification they shared was apparently the one that mattered most: loyalty to the queen.

Both appear to have been sworn to secrecy about the email diversions. Pagliano took the Fifth when called to testify before Congress. (Judicial Watch will get a crack at him at a deposition set for June 6.)

When career staffers at State raised concerns that Clinton’s email records weren’t being properly captured and preserved, they were told to shut up, according to the IG’s report, instructed “never to speak of the secretary’s personal email system again.”

Likewise, career staffers and contractors at the White House were ordered to keep those earlier unarchived emails secret. In fact, they testified that Callahan personally threatened them with jail time if they disclosed the gap to prosecutors or lawmakers.

A 1998 contractor audit of the White House email accounts affected by the “snafu” shows that much of the omitted email was addressed to top Clinton officials — including then-deputy counsel Cheryl Mills and other aides close to Hillary. A federal judge “excoriated Mills” for failing to get to the bottom of the missing emails, Fitton pointed out.

Now Mills finds herself in the middle of another investigation into the whereabouts of thousands of emails germane to investigations involving Hillary Clinton that also have conveniently turned up missing. After following Clinton to State, where she served as her chief of staff and counsel, Mills joined Clinton in flouting federal records-management requirements by using personal email accounts to conduct official government business. It was Mills who helped her old boss delete some 32,000 emails from the server Pagliano set up, claiming they were irrelevant to investigations.

Same inner circle, same MO. Recognize a pattern?

Paul Sperry is a former Washington bureau chief for Investor’s Business Daily and the author of “Infiltration” and “The Great American Bank Robbery.”

What is Hillary’s favorite footwear? Flip-flops!