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The Justice Department sent a letter to a Pennsylvania county on Thursday, ordering it to change its practices after multiple military ballots were found discarded.

The issue surfaced earlier in the day when the DOJ announced that it had recovered a small number of discarded ballots. While the Justice Department would not say where they had found the ballots, they did say there were nine recovered -- seven of which were cast for President Trump, while the other two were sealed by Luzerne County before the FBI recovered them,

In his letter to Luzerne County officials, U.S. attorney David Freed indicated that additional ballot materials were found in a dumpster. Freed said their investigation yielded "troubling" findings, including that the county allegedly improperly opened ballots.

PENNSYLVANIA ELECTION OFFICIALS SOUND ALARM OVER 'NAKED BALLOT' RULING, WARNING IT COULD JEOPARDIZE 100,000 VOTES

"Even though your staff has made some attempts to reconstitute certain of the improperly opened ballots, there is no guarantee that any of these votes will be counted in the general election. In addition, our investigation has revealed that all or nearly all envelopes received in the elections office were opened as a matter of course," Freed's letter read.

"It was explained to investigators the envelopes used for official overseas, military, absentee and mail-in ballot requests are so similar, that the staff believed that adhering to the protocol of preserving envelopes unopened would cause them to miss such ballot requests. Our interviews further revealed that this issue was a problem in the primary election--therefore a known issue--and that the problem has not been corrected," he added.

"While the assigned investigators are continuing their work including reviewing additional discarded materials, it is imperative that the issues identified be corrected."

On Monday, Luzerne County District Attorney Stefanie Salavantis requested the investigation, which involves cooperation with the FBI and the U.S. Attorney's Office. Her office claims it opened an investigation after hearing about issues surrounding the ballots last week, on Sept. 17.

Freed said that in additon to the military ballots, "investigators recovered four (4) apparently official, bar-coded, absentee ballot envelopes that were empty. Two (2) of those envelopes had the completed attestations and signatures on the reverse side.  One (1) envelope with a handwritten return address was blank on the reverse side. The fourth empty envelope contains basic location information and the words “affirmation enclosed” on the reverse side."

The majority of the recovered materials, he said, were found in an outside dumpster.

In a statement provided to Fox News, Chief County Solicitor Romilda P. Crocamo said: "Luzerne County thanks the Luzerne County District Attorney’s Office, the United States Attorney’s Office, the Federal Bureau of Investigations and the Pennsylvania State Police for quickly accepting our request and for their professional work in this matter. The County will continue to work in cooperation with the authorities throughout their review. Due to the fact that this is an ongoing investigation, it is not appropriate for the County to provide further comment at this time."

The incident touched on widespread concerns about election integrity amid social distancing restrictions that arose during the coronavirus. "It is the vital duty of government to ensure that every properly cast vote is counted," DOJ's release read.

Republicans have generally resisted calls for mail-in ballots due to concerns surrounding potential fraud and error. Democrats have pushed the mail-in alternative as a way to ensure voters can cast their ballots safely -- although Axios reported on Thursday that party leaders are increasingly pushing in-person voting.

That could be especially problematic for swing states like Pennsylvania, which Trump won by less than a percentage point.

Luzerne has been held up as an example of Trump's appeal to swing voters. He won the mid-state county after former President Obama won it during 2008 and 2012.

State election officials recently sounded the alarm that thousands of votes could be tossed out in November after a state Supreme Court ruling last week that "naked ballots" cannot be counted.

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The Court ruled that officials in the battleground state can reject mail-in ballots sent without a secrecy envelope, which prevents the poll workers from seeing how someone voted. The ruling rescinded previous guidance allowing counties to count "naked ballots," or those ballots not placed in the proper security envelope.

More than 100,000 ballots could be thrown out as a result of the decision, according to Lisa Deeley, the chair of the Philadelphia city commissioners. President Trump won Pennsylvania by just more than 44,000 votes during the 2016 election.

Fox News' Megan Henney contributed to this report.