The president responded quickly from his holiday home in Florida, via Twitter:

“Sorry Chief Justice John Roberts, but you do indeed have ‘Obama judges’, and they have a much different point of view than the people who are charged with the safety of our country. It would be great if the 9th Circuit was indeed an ‘independent judiciary’ …”

Trump was referring to the US Court of Appeals for the 9th Circuit, which covers much of the West Coast – although the ruling he was criticising came from a district judge in California, not the circuit court. Trump feels aggrieved by decisions of the appeals court, which he tweeted Wednesday has become “a terrible, costly and dangerous disgrace.”

Trump regularly says the 9th Circuit is the one most overruled by the Supreme Court, but that depends on the time period under consideration. Studies show that over the past five years, three others have a higher percentage of decisions overturned.

The rebuke-and-retort between the heads of two branches of the federal government astounded those who carefully watch the Supreme Court. Justices, and the chief justice in particular, hardly ever issue statements on news events.

Judge bars Donald Trump from denying asylum to people entering US illegally at Mexico border

But it appeared Roberts, when asked to comment by the Associated Press, was eager to counter Trump’s criticism Tuesday of District Judge John Tigar. The Roberts statement did not mention the president by name.

The chief justice is an aggressive defender of the judiciary and has frequently expressed concern about attacks on its impartiality, whether they come from the left or the right. In 2010, he called the timing of President Barack Obama’s criticism of the court’s decision in Citizens United v. FEC during the president’s state-of-the-nation speech “very troubling”.

Roberts made it clear last month that he is particularly sensitive about the image of the courts because of the recent partisan battle over the confirmation of Justice Brett Kavanaugh.

Supreme Court justices bristle at the suggestion they are not independent, despite Trump’s apparent confidence Tuesday that the setback in lower courts just means “we end up having to go to the Supreme Court, like the travel ban, and we won”.

At an event at the University of Minnesota just after Kavanaugh’s confirmation, Roberts said the court served “one nation” and not “one party or one interest”.

“Our role is very clear: We are to interpret the Constitution and laws of the United States, and to ensure that the political branches act within them,” he said. “That job obviously requires independence from the political branches. The story of the Supreme Court would be very different without that sort of independence.”

Wednesday’s statement from Roberts was the first time the chief justice has responded to criticism from the president, which at times has got personal.

During the 2016 campaign, Trump frequently disparaged Roberts, who was nominated by President George W Bush. Roberts has a solidly conservative voting record in his 13 years on the Supreme Court, but Trump labelled him an “absolute disaster” because of one vote: Roberts’ decision to join liberals in 2012 to uphold the Affordable Care Act, also known as Obamacare.

Donald Trump’s troops at US-Mexico border wonder what the mission is

In a tweet after the decision, Trump said Justice Anthony Kennedy “should be proud of himself for sticking to his principles, in light of Justice Roberts’ bull****!”

Trump on Tuesday had told reporters outside the White House that he had a “major complaint” about Tigar’s decision, in which the judge temporarily blocked the administration from denying asylum to migrants who illegally cross the southern border.

Tigar, of the Northern District of California, ruled late Monday that federal law clearly states that migrants can seek asylum anywhere on US soil.

“Whatever the scope of the President’s authority, he may not rewrite the immigration laws to impose a condition that Congress has expressly forbidden,” the judge, who was appointed by Obama, wrote in a 37-page ruling.

Trump erupted about the decision. “This was an Obama judge. And I’ll tell you what, it’s not going to happen like this anymore,” the president said. “Everybody that wants to sue the United States, they file their case in – almost – they file their case in the 9th Circuit. And it means an automatic loss no matter what you do, no matter how good your case is.”

Trump added: “We will win that case in the Supreme Court of the United States.”

In his Twitter response to Roberts on Wednesday, Trump again attacked the 9th Circuit, saying “a vast number” of its rulings on border and security issues are overturned. “We need protection and security – these rulings are making our country unsafe! Very dangerous and unwise!” he tweeted.

Both Roberts and Trump have supporting evidence for their arguments. Although Roberts – as well as Trump’s two nominees to the Supreme Court, Neil Gorsuch and Kavanaugh – decry any attempt to label judges as partisan, studies show there are clear ideological differences between judges nominated by presidents of different parties. That is why there are so many partisan battles over judicial nominations, and why the Trump administration has made filling the courts with conservative judges such a priority.

But Trump is fixated on the adverse rulings that come from the 9th Circuit, which is considered the nation’s most liberal regional appeals court. It is also the largest, covering nine states, and in his tweet, Trump again called for breaking it up, a proposal that has been debated for decades without resolution.

And Trump’s losing streak in lower courts is nationwide, with district judges and appeals courts across the country ruling against the administration’s policies on issues as diverse as immigration, abortion policy for teenage undocumented immigrants and how to judge the Commerce Department’s actions on the US census. Judges nominated by presidents of both parties have been part of those decisions.

Last week, the Trump administration was thwarted in its efforts to revoke CNN reporter Jim Acosta’s White House press credentials by US District Judge Timothy Kelly – a Trump appointee.

Because of the losses, the administration has pursued an aggressive agenda of trying to get the Supreme Court to take up the lower-court decisions before they have made a thorough but time-consuming journey through the appeals process.

Trump will need Roberts in those efforts, since the court now has five committed conservatives and four consistent liberals.

Roberts delivered the administration its biggest win at the Supreme Court at the end of the last term, when the court on a 5-to-4 vote upheld the president’s “travel ban” on people from certain Muslim-majority countries.

In ruling that the president had not exceeded his powers, the chief justice put aside comments that Trump had made about Muslims.

“The issue before us is not whether to denounce the statements,” Roberts wrote. “It is instead the significance of those statements in reviewing a Presidential directive, neutral on its face, addressing a matter within the core of executive responsibility. In doing so, we must consider not only the statements of a particular President, but also the authority of the Presidency itself.”

He added: “We express no view on the soundness of the policy.”