Is Eric Holder‘s Justice Department driven by a political agenda, or are the department’s recent prosecutorial decisions simply signs of overzealousness?

The Justice Department has focused on two prominent Republicans, announcing a corruption indictment of former Virginia Gov. Robert McDonnell and launching an active and very public criminal investigation into the antics of New Jersey Gov. Chris Christie’s administration. In doing so, federal prosecutors have created at least the appearance that they are targeting two men who have been touted as plausible candidates for the GOP presidential nomination in 2016.

A reading of the McDonnell indictment raises the obvious question of why the feds are charging someone who, as governor, engaged in conduct that is run-of-the-mill political activity in virtually all jurisdictions, but especially in states, like Virginia, whose laws quite clearly allow it. Certainly Mr. McDonnell and his wife, Maureen, don’t come off well in the indictment. She in particular is painted as greedy even by political standards. Both are charged with receiving expensive gifts as well as loans from businessman Jonnie R. Williams Sr., whose commercial dietary supplements were promoted by the governor. Mr. McDonnell and his wife also invited Mr. Williams to dinners and events at the governor’s mansion and arranged audiences for him with state health officials.

Mr. McDonnell’s legal team responded to the accusations in a blistering motion in federal court in Richmond on Jan. 21, the day the indictment was announced, asserting that the activities alleged against Mr. McDonnell are no different from those of political figures nationwide. To charge Mr. McDonnell on these counts would, according to the defense, suggest an “untested, novel construction of the federal bribery statutes” that would put every state—and, for that matter, federal—officeholder in jeopardy of federal indictment.

The defense motion points out that Anthony Troy, a former Democratic attorney general of Virginia, “conducted an in-depth investigation into this issue” and concluded that since Mr. Williams and his company “neither sought nor received any special benefits from any public official,” no crime was committed. Defense counsel argue that “political courtesies” extended to campaign donors or to generous friends are not crimes under any reasonable interpretation of the federal bribery statutes.

The attorney general testifies during a Senate Judiciary Committee hearing, Jan. 29. Getty Images

Were it otherwise, notes the unusually acerbic motion, “President Obama‘s recent visit to DreamWorks DWA +2.23% DreamWorks Animation SKG Inc. Cl A U.S.: Nasdaq $33.99 +0.74 +2.23% Jan. 30, 2014 4:00 pm Volume (Delayed 15m) : 698,835 AFTER HOURS $33.99 0.00 0.00% Jan. 30, 2014 5:22 pm Volume (Delayed 15m): 5,084 P/E Ratio N/A Market Cap $2.79 Billion Dividend Yield N/A Rev. per Employee $319,704 34.5034.0033.5033.0010a11a12p1p2p3p4p5p 01/17/14 Tiny Animated Film ‘Ernest & C… 12/16/13 IPO This Week for Sergio Leone… More quote details and news » studio in Hollywood, a company run by one of his top donors,” would put Mr. Obama into the same club as Mr. McDonnell. As much could be said of every president who has awarded ambassadorships to campaign donors.

The investigation into the Christie administration by U.S. Attorney Paul Fishman (a registered Democrat) likewise raises eyebrows. The story is by now familiar: In the run-up to the New Jersey gubernatorial election, the Christie administration asked the mayor of Fort Lee, Democrat Mark Sokolich, to support the governor’s re-election bid. Mr. Sokolich declined. In return, it is alleged that Mr. Christie’s office coordinated with the Port Authority of New York and New Jersey to invent a four-day traffic study that closed two lanes approaching the George Washington Bridge, thereby creating epic traffic jams in Fort Lee.

Further suspected wrongdoing involves claims that the Christie administration abused its power to distribute federal disaster funds after Hurricane Sandy, withholding funds from another Democratic mayor who wasn’t being sufficiently helpful with a development project favored by Mr. Christie.

The notion that a federal felony is committed when state officials reward political friends and punish enemies in this manner has become surprisingly widespread within the Justice Department. Because of vague and broad federal criminal statutes, there isn’t much in public or political life these days that is not an arguable ground for an indictment. Obviously lost on federal prosecutors is the irony that their prosecutions of state politicians often create the same appearance of bias that the feds consider criminal when it is seen at the state and local level.

With the careers of two popular Republican governors—who might have been destined for national office—hanging in the balance, such suspicions of federal prosecutorial partisanship have become inevitable. But given that such federal prosecutions for state political activities abound, one must not be too quick to conclude that the department’s motives are purely partisan. There may be some nonpartisan recklessness too.

Consider Justice’s behavior in Massachusetts, a state dominated by a long-entrenched Democratic political machine that also has a U.S. attorney championed by Ted Kennedy and appointed by Barack Obama. Former state probation department officials are about to go on trial for awarding jobs to candidates sponsored by Democratic state legislators in exchange for support in departmental appropriations. U.S. Attorney Carmen Ortiz is applying a bizarre theory of criminality to this patronage—and her efforts recently received a black eye when it was learned that recommendations for hiring positions were made not only by state legislators, but also by judges and even the chancellor of Boston College, the Rev. J. Donald Monan.

There’s no telling whether the feds can succeed in criminalizing “politics as usual” in a state where the legislature and judiciary have routinely failed to adopt the Justice Department’s prescription for an acceptable political culture. What has become clear, however, is that the department’s war against local politicians will continue, and that its motivations will lie somewhere between the quest for federal power and partisan politics.

Mr. Silverglate is the author of “Three Felonies a Day: How the Feds Target the Innocent” (Encounter Books, updated in paperback 2011).