The surprise decision to appoint a special prosecutor to oversee the FBI's investigation into Russia’s meddling in the presidential election is throwing ongoing congressional probes into limbo.

Senators are scrambling to figure out what Deputy Attorney General Rod Rosenstein’s decision to name former FBI Director Robert Mueller as a special counsel means for their own investigations.

Lawmakers have been working for months to sort through documents and line up interviews with former Trump officials and have even issued a subpoena against former national security adviser Michael Flynn, who resigned earlier this year.

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“I think it pretty well at a minimum limits it, maybe just takes us out of the game,” Sen. Lindsey Graham Lindsey Olin GrahamThe Hill's Campaign Report: Arizona shifts towards Biden | Biden prepares for drive-in town hall | New Biden ad targets Latino voters Senate Democrats' campaign arm announces seven-figure investment to boost Graham challenger Graham: Comey to testify about FBI's Russia probe, Mueller declined invitation MORE (R-S.C.) said Thursday. "It’s going to be hard for us. … Public access to what happened is going to be very limited now because of a special counsel and I don’t want to get in his way."

Sen. Christopher Coons Christopher (Chris) Andrew CoonsBiden promises Democratic senators help in battleground states Shakespeare Theatre Company goes virtual for 'Will on the Hill...or Won't They?' The Hill's Morning Report - Sponsored by The Air Line Pilots Association - Pence lauds Harris as 'experienced debater'; Trump, Biden diverge over debate prep MORE (D-Del.) added his “concern is that we do not end up in a place where the special counsel doesn’t communicate with Congress for months or years.”

Graham and Coons are both members of the Senate Judiciary Committee, one of four congressional committees digging into Russia’s election interference and possible ties to Trump campaign officials. The Senate Intelligence, House Intelligence and House Oversight committees are also conducting investigations.

Senators raised questions about how they might coordinate their investigations with the FBI and Justice Department probes with Rosenstein during a closed-door briefing Thursday.

Mueller is effectively taking over an ongoing FBI investigation into Russia's election meddling and any contacts between the Trump campaign and Moscow.

But his special prosecutor title leaves him largely unaccountable to Congress, raising concerns among lawmakers that he could limit what documents the congressional investigations receive or who can appear before their committees.

“There were a number of members of the Judiciary and Intelligence committees that raised concerns about access to information, and the processes that would be put in place to expeditiously get that information,” Sen. Jeff Merkley Jeffrey (Jeff) Alan MerkleyThe Hill's Morning Report - Sponsored by The Air Line Pilots Association - Trump, Biden renew push for Latino support Sunday shows - Trump team defends coronavirus response Oregon senator says Trump's blame on 'forest management' for wildfires is 'just a big and devastating lie' MORE (D-Ore.) told reporters after the closed-door meeting.

Leadership in both parties, as well as top lawmakers on the committees running the investigations, quickly threw their support behind continuing the Senate Intelligence Committee’s investigation.

Senate Majority Leader Mitch McConnell Addison (Mitch) Mitchell McConnellMcConnell focuses on confirming judicial nominees with COVID-19 talks stalled McConnell accuses Democrats of sowing division by 'downplaying progress' on election security Warren, Schumer introduce plan for next president to cancel ,000 in student debt MORE (R-Ky.) has repeatedly argued publicly that a special prosecutor wasn’t needed and that he supported the probe by the Senate Intelligence Committee, which he is an ex officio member of as the chamber’s top Republican.

Sen. Dick Durbin Richard (Dick) Joseph DurbinMcConnell focuses on confirming judicial nominees with COVID-19 talks stalled Senate Republicans signal openness to working with Biden Top GOP senator calls for Biden to release list of possible Supreme Court picks MORE (D-Ill.) noted that McConnell was one of the first members to ask Rosenstein about how to coordinate the investigations during Thursday’s meeting.

Washington has a long history of naming special counsel to dig into White House controversies. Former President Bill Clinton William (Bill) Jefferson ClintonD-Day for Trump: September 29 Trump job approval locked at 42 percent: Gallup If Trump doesn't know why he should be president again, how can voters? MORE’s administration was plagued by yearslong investigations, ultimately leading to his impeachment trial five years later.

Republicans also wanted special counsel to look into former Secretary of State Hillary Clinton Hillary Diane Rodham ClintonHillicon Valley: FBI chief says Russia is trying to interfere in election to undermine Biden | Treasury Dept. sanctions Iranian government-backed hackers The Hill's Campaign Report: Arizona shifts towards Biden | Biden prepares for drive-in town hall | New Biden ad targets Latino voters FBI chief says Russia is trying to interfere in election to undermine Biden MORE's private email server, even though Congress had its own investigation.

Senators stressed that they’re still in the game in the wake of Rosenstein's decision.

"We still have an extremely important role to play," Sen. Susan Collins Susan Margaret CollinsThe Hill's Campaign Report: Biden asks if public can trust vaccine from Trump ahead of Election Day | Oklahoma health officials raised red flags before Trump rally Gideon leads Collins by 12 points in Maine Senate race: poll Senate leaders quash talk of rank-and-file COVID-19 deal MORE (R-Maine) told MSNBC. "Our investigation is really important because it is, it will be in public. His won't. And we need a far broader set of the facts to come out.”

Sens. Richard Burr Richard Mauze BurrRep. Mark Walker says he's been contacted about Liberty University vacancy Overnight Defense: Trump rejects major cut to military health care | Senate report says Trump campaign's Russia contacts posed 'grave' threat Senate report describes closer ties between 2016 Trump campaign, Russia MORE (R-N.C.) and Mark Warner Mark Robert WarnerIntelligence chief says Congress will get some in-person election security briefings Overnight Defense: Trump hosts Israel, UAE, Bahrain for historic signing l Air Force reveals it secretly built and flew new fighter jet l Coronavirus creates delay in Pentagon research for alternative to 'forever chemicals' House approves bill to secure internet-connected federal devices against cyber threats MORE (D-Va.), the chairman and vice chairman respectively of the Senate Intelligence Committee, also signaled that their committee's probe would continue to move forward in the immediate wake of Rosenstein's announcement.

Warner said on Thursday afternoon that he and Burr want to sit down with Mueller as soon as next week to try to “deconflict” the jurisdictional boundaries of their investigations.

“In many ways our purview is broader than what may be some of the Justice Department/FBI investigation," he told reporters, defending the need to continue the congressional investigations.

Mueller was given control of the investigation into any coordination between the campaign and Russia but also any other matters that “may arise directly from the investigation” — such as FBI Director James Comey’s dismissal.

The Senate Intelligence Committee has also struggled to get Flynn to comply with its investigation. It is unclear what, if anything, lawmakers could do to force him to meet with the committee.

Sen. Ron Wyden Ronald (Ron) Lee WydenGOP senator blocks Schumer resolution aimed at Biden probe as tensions run high Republican Senators raise concerns over Oracle-TikTok deal Hillicon Valley: TikTok, Oracle seek Trump's approval as clock winds down | Hackers arrested for allegedly defacing U.S. websites after death of Iranian general | 400K people register to vote on Snapchat MORE (D-Ore.) said he would “go to the mat” to make sure the subpoena was followed, but Sen. Dianne Feinstein Dianne Emiel FeinsteinSenators offer disaster tax relief bill Democrats back away from quick reversal of Trump tax cuts Congress must save the Postal Service from collapse — our economy depends on it MORE (D-Calif.), the former chairwoman of the committee, hedged, telling reporters, “Frankly, he has rights.”

Graham echoed Feinstein, saying Flynn has a “Fifth Amendment right to not incriminate himself.”

“If I were his lawyer I would probably be making the argument that if I’m under criminal investigation, you cannot force me to compromise myself,” he added.

Senators also appeared uncertain on Thursday about what the Mueller pick meant for their push for Comey to testify publicly.

Lawmakers were already locked in a turf war over who would get Comey’s first public comments since he was fired.

"It looks like there's a little competition for jurisdiction, but truthfully both the Judiciary Committee and the Intelligence Committee have some say in all of that," said Sen. John Cornyn (R-Texas), who is a member of both committees.

The Judiciary Committee has requested any memos from Comey and any White House records of his conversations with Trump. Sen. Chuck Grassley Charles (Chuck) Ernest GrassleySenate Republicans signal openness to working with Biden Senators offer disaster tax relief bill Trump spikes political football with return of Big Ten season MORE (R-Iowa), who oversees the committee, said it would go forward with those requests.

But Graham signaled on Thursday that he wasn’t sure Comey would be able to come speak before Congress, specifying that he hasn’t yet heard from from the former FBI director.

“I don’t know if, one, if he wants to, [but] he has a reason now because there's a special counsel,” Graham told reporters. “It probably shuts us down”

Sen. Dick Durbin (D-Ill.) added, “I don’t know the answer to that. I can’t tell you. I understand what Lindsey’s saying. I would like to hear from Comey.”

“We're gonna have to put him on a milk carton,” Graham said. “'Have you seen this man?'"