WASHINGTON — When the White House first released the reconstructed transcript of President Trump’s July 25 phone conversation with the president of Ukraine, some former government officials noticed something peculiar about it.

The document lacked a standard marking in its upper right-hand corner, known as a “package number,” or the number that the National Security Council officials would assign to the transcript as they logged it for storage.

Instead, it bore the marking “[PkgNumberShort],” which former officials, including one who served in the Trump White House, said was an indication that the document had not been formally placed into the council’s carefully organized records system according to normal practice.

The full meaning of that became clear on Thursday only with the release of the complaint by an anonymous whistle-blower brought against Mr. Trump. The complaint explained that the transcript of the call between Mr. Trump and the Ukrainian president, Volodymyr Zelensky, was handled in a highly unusual manner, stored not in the National Security Council’s main computer system but in a far more secret and restricted system maintained by intelligence officials within the White House.

The whistle-blower, whom The New York Times has identified as a C.I.A. officer who was detailed to the White House, alleges that the National Security Council took an extra and previously unknown step to shield Mr. Trump’s call with Mr. Zelensky from all but a very small number of officials by assigning it to that system.

The rough transcript of Mr. Trump’s call with Mr. Zelensky was stored in a the system operated by the agency’s intelligence directorate “solely for the purpose of protecting politically sensitive — rather than national security sensitive” information, the whistle-blower wrote. He added that White House officials told him it was “not the first time” Trump officials had confined a presidential transcript that way.

The more secure system is designed to hold delicate information about covert actions, intelligence programs and other highly classified activities, several former National Security Council officials said. Records of presidential calls with foreign leaders would be stored there only rarely, they said, in cases where those topics were discussed with close American partners like the leaders of Britain and Israel.

Accessing that special database requires enhanced desktop computer software not granted to all National Security Council officials. In extreme cases, agency aides must physically enter the offices of the intelligence directorate to read documents stored in the system. In the Obama White House, delicate documents were often hand delivered in a thick leather folder bearing the National Security Council seal and had to be returned.

The handling of the Ukraine call transcript has raised alarms among Democrats in Congress and former national security officials of both parties, including ones who served in the Trump administration. They agreed that nothing about the conversation appears to warrant placement in the extra-secure system.

“We need to look into the allegation that this may not be the only communication of a potentially corrupt character that was shielded by this classified information computer system abused for that purpose,” Representative Adam B. Schiff, Democrat of California and the chairman of the House Intelligence Committee, told reporters on Thursday at the Capitol.

Mr. Schiff and other Democrats say it appears that the White House sought to hide Mr. Trump’s effort to pressure Mr. Zelensky to investigate former Vice President Joseph R. Biden Jr., a possible opponent in the 2020 presidential election, and his son Hunter Biden, as well as to pursue conspiracy theories that hold that Russia did not meddle in the 2016 presidential election.

“During my tenure, I had no knowledge of documents being moved out for political sensitivity,” said a former Trump White House official familiar with the system. “I don’t know the legality of what was done. It certainly feels unethical.” The official said that decisions to move documents to different levels of classification typically involve the National Security Council’s legal office.

All officials at the agency, whose size has ranged from about 100 to 150 staff members in recent years, have security clearances that allow them access to a shared classified computer network on which countless documents are stored, many of them categorized at relatively low levels of secrecy.

Stored on the less-classified network are transcripts of presidential calls with foreign leaders, which past White Houses have actively distributed widely among national security and foreign policy officials on secure email systems.

After embarrassing leaks in 2017, in which two transcripts of Mr. Trump’s calls with foreign leaders were published in the news media, the Trump White House cut the number of people to whom phone call records were distributed.

In the case of Mr. Trump’s call with Mr. Zelensky, White House officials appear to have concluded that it was not enough to limit distribution of the document, and made it impossible to read by all but a select few N.S.C. staff members. They did so by housing it in the far more restricted system, which requires software that most officials do not have.

Even those White House aides granted access to the more secret system must have specific permission to read individual documents there, which are known as Sensitive Compartmentalized Information and organized by code words. One former agency staff member said that in the most extreme cases, it might be necessary for an aide to physically visit the intelligence directorate to read certain documents.

Larry Pfeiffer, a former career intelligence official who served as White House Situation Room director during the Obama administration, said that the risk of political embarrassment is not adequate grounds for placing an N.S.C. document in a system designed for national security matters like the operation to kill Osama bin Laden.

“Clearly, someone made a decision that this conversation needed to be locked down,” Mr. Pfeiffer said. “You read this conversation and there is nothing ‘compartmented’ from an intelligence perspective.”

“Anyone with half a brain can read it and understand why they wanted to protect the distribution,” he added.

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