BOCA RATON, Fla. -- Major League Baseball officials impeded a Florida Department of Health investigation of Biogenesis founder Tony Bosch by purchasing clinic documents they likely knew had been stolen and had been warned not to obtain, sources close to the investigation told "Outside the Lines."

The Department of Health closed its case on Bosch, who is not licensed to practice medicine, in April with a $5,000 fine and cease-and-desist letter. On July 31, Bosch signed an agreement with health officials reducing the penalty to $3,000.

A state official said the limited scope of the investigation and its conclusion were direct results of MLB officials purchasing documents related to the since shuttered clinic at the center of a performance-enhancing drug scandal involving Alex Rodriguez, Ryan Braun and at least a dozen other players.

The source said MLB knew the documents had been intended for Florida investigators and that the purchase of them hindered the state investigation by preventing the department from gathering additional evidence against Bosch, doctors and others affiliated with the clinic. Further, MLB officials never told health department officials they had obtained the records, the source said.

"They can't say they weren't warned," the official said.

The allegation that MLB affected an official investigation is just the latest in a high-stakes drama that has come down to a battle between Rodriguez, the game's highest-paid player, and baseball leadership.

For more than a year, investigators for Major League Baseball and Rodriguez have thrown tens of thousands of dollars at potential witnesses and tried various strong-arm tactics in pursuit of patient and clinic medical records. The documents have been key to Rodriguez's arbitration hearing over his 211-game suspension. The hearing resumes Monday in New York.

Tony Bosch, right, initially denied knowledge of suspected PED distribution at Biogenesis -- his since closed South Florida clinic -- before agreeing to cooperate fully with baseball's investigation. ESPN

An MLB official denies impeding the Florida Department of Health investigation while also suggesting repeatedly that the health investigation was more a regulatory than criminal undertaking and therefore not as serious. A source told "Outside the Lines" the health department ultimately stepped aside from its investigation at the request of federal investigators, but that was after MLB had purchased the documents. The MLB official said its investigators have continued to cooperate with subsequent criminal investigations by the Miami-Dade State Attorney's Office and the U.S. Attorney's Office, which are focused on a cadre of Bosch associates, doctors and pharmacies.

The same MLB official acknowledges its own Biogenesis investigation would have been "extremely impeded" without the Biogenesis documents, telling "Outside the Lines" that without the documents and Bosch's subsequent cooperation "nobody would have been disciplined."

More than a dozen minor and major league players have been suspended for their roles in the Biogenesis case, with only Rodriguez fighting the discipline.

Florida Department of Health spokesman Nathan Dunn refused to answer questions and declined to comment to "Outside the Lines" on multiple occasions in recent weeks but issued a statement Friday evening, several hours after ESPN.com published this story: "The Florida Department of Health was able to complete its investigation and took the appropriate action allowed by law against Mr. Bosch." Dunn declined further comment.

The health department's unlicensed activities office, which was the first group to investigate Biogenesis, polices a broad spectrum of medical practitioners in the state, including those unlicensed who portray themselves as doctors and nurses. With more egregious infractions, the investigators work with local authorities to bring criminal charges.

Sources told "Outside the Lines" that MLB obtained the documents at two different times through the work of Dan Mullin, who leads MLB's Department of Investigations. He gave $100,000 in cash to Gary Jones, a 54-year-old South Floridian with a criminal past, in March in exchange for four computer flash drives containing documents. Jones was a friend of Biogenesis whistle-blower and former employee Porter Fischer, who originally took the documents from the South Florida clinic.

A second set of documents -- the batch slated to go to the Florida health department -- was stolen from Fischer's car March 24. On April 16, Jones pocketed another $25,000 for those files. It's unclear how he came in possession of them.

According to an affidavit Jones signed at the bequest of Rodriguez's legal team in September, Jones acknowledged obtaining documents stolen from Fischer's car and later selling them to MLB. Boca Raton police have since reopened their investigation into the theft, and sources said Jones is of particular interest after having denied in an April 18 police interview that he had any knowledge of the break-in or had even spoken with a representative of MLB, though baseball officials have said by that date they had already met with Jones twice and paid him.

An MLB official said baseball had no idea it purchased stolen documents, emphasizing, "[Jones] didn't tell Dan Mullin he had stolen documents."

But at least one person affiliated with MLB's investigation had an idea police were seeking information about a crime related to the documents. Police records indicate that Kevin O'Rourke, an outside investigator retained by MLB, contacted Boca Raton police about the break-in April 12 and got a call back from the lead detective April 17 -- a day after Mullin gave Jones the second payment.

MLB officials, who said they never asked Jones to put in writing where or how he obtained the documents, said they were operating under an assumption that Fischer and Jones were working together, with Jones acting as his then-friend's agent in selling the documents.

"And they kind of staged this whole break-in, because Porter Fischer couldn't sell the documents himself because [MLB had a court order preventing Fischer from selling, transferring or destroying the documents]," an MLB official told "Outside the Lines."

MLB made the second document purchase "because there were different documents in there that were relevant to our case," the official said.

Repeated messages left for Jones by "Outside the Lines" went unreturned.

Even today, the MLB suspicion remains that Fischer got a cut from the money paid to Jones.

At the time of the late March break-in, MLB officials had grown exasperated attempting to purchase documents from Fischer. They walked after he snubbed a $125,000 offer sent via text March 18, which followed prior offers of $15,000 and then $60,000. Their frustration came from the belief that the files could go a long way in cementing their case.

Fischer described the notion he and Jones worked together as "absolutely crazy," portraying himself as having been betrayed by Jones and two other friends.

"Let me ask, then, why would I have turned down their offer for $125,000 five days before [the car break-in]?" Fischer said. "I turned them down at every stage. So they want to say I gave this to [Jones]? And that is why I immediately called the cops? ... That is why I've been jumping up and down to the feds and the state government? That I knew the [guy] stole from my car? Really. That is baseball's theory? Go for it, dude. Prosecute me. And let's find every single accessory that was involved. I need to know. This is bulls---."

Before dealing with Jones, MLB had tried to lean on the Florida Department of Health as a source for documents and information. But it faced obstacles in teaming with an investigating agency. If the state had taken possession of Fischer's documents, it is likely MLB would have had to wait until that investigation played out. And because the bulk of the files pertained to patient records, it's uncertain whether the files could have been shared with a nongovernmental investigation.

Sources told "Outside the Lines" a state health official had confirmed the validity of what Fischer possessed, plus MLB had already paid the whistle-blower $5,000 early this year for a sample of the files -- which connected two MLB players and a retired NFL player to Bosch's wellness clinic.