Walker's recall campaign and other conservative groups have been investigated since 2012 as part of the secret probe. The investigation focused on alleged illegal campaign fundraising, spending and coordination between conservative groups, Walker's campaign and others during recall elections in both 2011 and 2012.
No charges have been filed.
Last month U.S. District Judge Rudolph Randa issued a preliminary injunction halting the investigation, saying it violated the First Amendment rights of Wisconsin Club for Growth and one of its directors, Eric O'Keefe, who was among the targets of the probe.
Prosecutors filed briefs in the 7th U.S. District Court on Wednesday in support of their request that Randa's order halting the investigation be put on hold. Prosecutors are also appealing the judgment.
As part of their motion, prosecutors filed a partially redacted copy of a petition submitted in July by Iowa County District Attorney Larry Nelson requesting that the secret John Doe investigation be commenced against O'Keefe.
Nelson said it was important to keep the investigation secret because any public filing "will generate substantial publicity, both from traditional (e.g., print and broadcast journalism) and non-traditional (e.g. Internet blog) information sources," Nelson said. "This is because the individuals involved in this investigation are well placed."
One line of the filing is blacked out immediately after that statement.
Randa, in his May order halting the investigation, said the investigation was looking into Walker's recall committee and "all or nearly all right-of-center groups and individuals in Wisconsin who have engaged in issue advocacy from 2010 to the present."
Randa's order, other court filings and public statements by O'Keefe and others have revealed many details about the investigation since it first publicly became known in October. A coalition of media groups, and prosecutors, have agreed that all records related to the case that don't contain private information should now be made public since so much is already known about the investigation. But Wisconsin Club for Growth has asked that hundreds of pages remain secret.
Back in July when the probe was still unknown to the public, Nelson argued that continued secrecy was "important to its success." He said that publicity would warn possible witnesses, resulting in "statements that are less likely to be entirely candid."
He also said publicity could result in records being lost or destroyed, and cause the reputation of innocent people to be unfairly damaged if they are never criminally charged.
John Doe investigations are done largely in secret and overseen by a judge. Prosecutors can collect evidence and compel people to testify, but the activity is largely shielded from the public.
Retired Kenosha County Judge Barbara Kluka, who was overseeing the probe at the time of the July filing, issued an order in August authorizing commencement of the John Doe investigation against O'Keefe on the grounds that crimes may have been committed. Two lines of that order, which prosecutors included in their Wednesday filing, were blacked out.
O'Keefe's attorneys have denied any wrongdoing.