In a case that could help shape transparency rules in a digital era, a court on Wednesday said the European Union should not have denied a journalist’s request for text messages exchanged as a top official negotiated for coronavirus vaccine access.

The case centered on the European Commission’s denial of the request, from a New York Times journalist, for text messages between Ursula von der Leyen, president of the commission, and Pfizer’s chief executive, Dr. Albert Bourla. The two had exchanged the texts in 2021 while striking a deal for Covid-19 vaccines.

When the commission refused to provide the messages, The Times in early 2023 brought a case challenging that decision in court.

The question at the core of the case was whether Ms. von der Leyen’s text messages were covered by E.U. transparency laws and should have potentially been released.

While the commission had said that it could not find the messages in question, it never explained how extensively it had searched for them; it simply argued that text messages are “short-lived” by nature and do not contain important information that would require them to be retained and disclosed. It remains unclear whether the messages still exist or whether they have been deleted.

The General Court in Luxembourg ruled that the commission did not provide enough explanation in refusing the request.

“The commission cannot merely state that it does not hold the requested documents but must provide credible explanations enabling the public and the court to understand why those documents cannot be found,” the court said in a news release.

The commission also “failed to explain in a plausible manner” why it thought that messages exchanged on such a major issue — the procurement of vaccines for a public health crisis — did not contain important information, the court added.

The European Commission can appeal the verdict.

In a statement, the commission said it would “adopt a new decision providing a more detailed explanation.”

The New York Times said the ruling sent a message that “ephemeral” communications like text messages were not beyond the reach of public scrutiny.

“Today’s decision is a victory for transparency and accountability in the European Union,” Nicole Taylor, a spokeswoman for The Times, said in a statement.

Broadly, the case raised questions about how much the public should know about negotiations that cost taxpayers money and shape public policy.

The verdict comes at an important moment for the European Commission’s reputation for disclosure. Ms. von der Leyen began her second five-year term as leader of the commission, the bloc’s executive arm, late last year, and she has made standing up for core values like democracy and transparency key to her image.

“It’s a case about transparency, but ultimately, it’s a case about accountability,” said Nick Aiossa, director of Transparency International E.U., an anticorruption group.

The ruling is the culmination of years of back-and-forth.

The Times’s former Brussels bureau chief, Matina Stevis-Gridneff, reported in April 2021 that Ms. von der Leyen and Dr. Bourla had been exchanging texts and calls for a month as they negotiated over access to Covid vaccines.

After reading that article, Alexander Fanta, then a reporter at a German news outlet, filed a freedom-of-information request with the commission asking for the text messages. He was not given them. The E.U. ombudsman criticized that move, arguing that the commission had engaged in maladministration by not adequately searching for the text messages in response to the request.

But the commission did not back down.

The Times and Ms. Stevis-Gridneff followed up with a similar request for the messages. When access to the messages was refused, they took the commission to court.

Bloc representatives have not said whether anyone at the commission other than Ms. von der Leyen reviewed the contents of the messages. At one point the commission said it could not find the relevant messages.

Paolo Stancanelli, a lawyer representing the commission, said during a hearing in November, “I am not able to tell you until when they existed, or if they still exist.”

When both sides laid out their cases in Luxembourg at that hearing, lawyers for The Times argued that the European Commission actively encouraged staff to use disappearing text messages.

The Pfizer messages drew attention in part because they were about a subject of great public interest — the deal for Covid vaccines.

The agreement with the drug company was one of the biggest procurement contracts in European Union history. It was hailed by many as a success; through it, the bloc managed to secure 1.8 billion doses, enough to push up vaccination rates across the European Union.

Still, the commission has been dogged by transparency complaints surrounding the vaccine negotiations.

The commission has published redacted purchasing agreements but has not disclosed the full terms of the contracts it secured for Covid vaccines. It has said it needs to strike a balance between making information public and satisfying the legal requirements of the vaccine contracts.

Issues surrounding the text messages served only to deepen concerns about disclosure.