It is bad enough that the Trump administration blocked a federal criminal investigation when an Immigration and Customs Enforcement (ICE) agent killed Renee Good as she was turning her car away from him in Minneapolis the past January. Just before the shooting, Good and her partner had been observing and protesting against ICE officers.

Instead, it turns out the administration has been investigating progressive and even mainstream groups that have been involved in protests against Donald Trump’s sweeping deportations, according to newly released government documents.

That Trump’s deportations have prompted widespread outrage is hardly surprising. The president arguably had an electoral mandate to secure the US-Mexican border but not to raid workplaces and neighborhoods to deport undocumented immigrants.

Most such immigrants in the United States are now settled. They have been in the country for more than five years, and many have US-citizen children, work at regular jobs, pay taxes and are active members of their communities. Few Americans want their neighbors or work colleagues summarily deported.

In January, Minnesota was an epicenter of Trump’s deportation efforts. He deployed about 3,000 federal agents to this blue state to comb the streets in search of immigrants to deport. The public soon took to the streets in opposition, with some protesters using their phones to record detentions while others sounded the alarm that Trump’s agents were in the vicinity.

Yet rather than conduct an inquiry into the deportation agents’ often-unbridled violence, the administration turned its prosecutorial sights on the protesters. In what it called “Operation Puppet Master”, it used its enormous investigative powers to pursue a vendetta against an array of groups that opposed its deportation agenda.

Federal investigators justified the investigation by claiming that these groups might have provided help and money to the allegedly “violent opportunists and agitators” on the street. They also claimed that these groups provided “domestic terrorist financing”. This language parallels Trump’s directive last September expanding the definition of domestic terrorism to include using violence or intimidation to obstruct the rule of law.

Even if violence or other lawlessness occasionally broke out among the protesters, it is a huge leap to suggest that civic groups were criminally complicit. Federal conspiracy law is broad but not limitless. It requires two or more people to agree to commit a federal crime and for the accused to join that agreement.

It would hardly be surprising that various progressive groups banded together to monitor and oppose Trump’s deportations. But those activities are protected by the first amendment to the US constitution. They are completely lawful.

For the Trump administration to transform coordinated protests into a criminal conspiracy, it would have to show that the targeted groups knew the protests would obstruct federal agents “by force, intimidation or threat” and that such criminality was a purpose of their coordination. That is an enormous stretch.

The role of federal prosecutor is powerful. A prosecutor can destroy a target’s life with the reputational sting and financial burden of a criminal prosecution. Before I joined Human Rights Watch, I served for more than four years in the 1980s as a federal prosecutor, mainly in New York City. My experience was that most federal prosecutors were aware of their power and tried to wield it in good faith.

Trump’s criminal hounding of groups that oppose him shows no such deference to the requirements of justice.

The first warning sign was that the Trump administration didn’t even use the justice department or its FBI, which traditionally pursue criminal investigations. Even though Trump has decimated the department, sparking the departure of many career officials who refused to be tainted by the president’s personal vendettas and politicized prosecutions, the administration chose instead to deploy the Department of Homeland Security.

The DHS in turn issued administrative subpoenas, which do not require judicial authorization, and used other intrusive techniques to collect records and wire transfers from certain progressive groups going back three years – long before the anti-deportation protests began. That suggests what prosecutors refer to as a fishing expedition – the abuse of prosecutorial powers, in the absence of concrete evidence of wrongdoing, in the blind hope that something untoward might surface.

Undercover federal investigators also spied on public meetings and even infiltrated group chats on Signal as activists discussed protests and their political opinions. Agents recorded license plate numbers to determine who was attending protest meetings.

For example, at a 31 January meeting in a Minneapolis library, a homeland security undercover officer listened as supporters of a progressive climate group, the Sunrise Movement, discussed sit-ins, de-escalation tactics, and “having a police liaison and safety marshal present during events”. The agent at least had the honesty to report back that the Sunrise Movement organization focused on “peaceful” protests.

However, the Trump administration has charged 15 people with obstructing federal immigration operations in Minnesota using vehicles and other objects. The 94-page indictment does not allege injuries to specific ICE officers or serious violence, but asserts that activists set up blockades around government buildings, threw chunks of ice at federal vehicles and “stalked” agents. Similar charges in parallel cases have already been dismissed or dropped at an unusually high rate.

So far, none of the groups under investigation has been criminally charged, but prosecutors showed a grand jury a PowerPoint slide claiming that 18 groups were part of a conspiracy to impede Trump’s deportation agents in Minnesota.

The broad investigation brings back memories of a prior example of egregious federal misconduct targeting perceived leftist groups. Under the notorious J Edgar Hoover, the FBI from the 1950s to the 1970s conducted Cointelpro to infiltrate and discredit leftist organizations, especially those that promoted Black civil rights or opposed the Vietnam war. Exposure of these outrages led to major reforms, which the Trump administration now seems determined to reverse.

Many hope that the coming midterm elections in November will repudiate Trump’s lawlessness. Republicans are at risk of losing one or both houses of Congress. Yet this apparent abuse of criminal investigative powers reminds us that the presidency is powerful even without the legislative power of Congress.

Fortunately, the judicial system has managed to halt much of Trump’s deportation overreaching. Even grand juries, which traditionally show enormous deference to prosecutors, have been rejecting requests to bring charges. Moreover, while politicized federal prosecutors have ignored much of the misconduct by Trump’s deportation agents, some state prosecutors have tried to pick up the ball.

Yet much remains to be done as Trump seems determined to find ways to evade even adverse supreme court judgments. Exposure by journalists, protests by civic groups and outrage by the public are often the only tools we have.

Responding to the Trump administration’s misconduct, Unidos MN, a human rights group in Minnesota, said that the government is “lashing out desperately in hopes of intimidating people and organizations that have shown the power of communities acting together”. This latest Trump abuse shows the importance of continuing to stand up to his lawless vision of his presidency.

• Kenneth Roth is a Guardian US columnist, a senior fellow at Yale University and a former executive director of Human Rights Watch. He is the author of Righting Wrongs: Three Decades on the Front Lines Battling Abusive Governments