Hillary Clinton's private emails discussing the case of an Iranian scientist who was allegedly working with the U.S. could make it more difficult for the intelligence community to gain the trust of sources in the future, according to experts.

Shahram Amiri was an Iranian scientist who is believed to have given the U.S. information about Iran's nuclear program. After entering the Pakistan embassy and declaring he wanted to go home, Amiri left America in 2010 to return to Iran, where he was recently executed for treason.

Amiri appears twice in Clinton's emails, which were sent on her personal, unclassified server and released by the State Department, but never by name. The first on July 5, 2010, states that "our friend" needs to be given a way to leave the U.S. The second, a week later, says that the "gentleman" was still trying to get home and could "lead to problematic news stories."

Amiri's relationship had been reported publicly before the release of the emails. A 2010 New York Times story quoted U.S. officials who said Amiri was paid $5 million for giving information about the country's nuclear program to the CIA.

Still, Matthew McInnis, a resident fellow at the American Enterprise Institute, said he expects this revelation to have some impact on the intelligence community's ability to recruit sources, noting that doing so is already difficult and risky enough because of the vulnerabilities of electronic communication.

"I think if people know that senior U.S. officials are frequently talking about certain sensitive issues like this in unclassified emails, I think that would send a signal of how risky it is," he said.

Elizabeth Trudeau, a State Department spokeswoman, dodged questions Monday about whether the emails discussing Amiri may have played a role in his execution at the hands of the Iranian judiciary.

"We're not going to comment on what may have led to this event," Trudeau said.

"I couldn't speak to Iranian judicial procedures related to this specific case," she added. "We've made our concerns known writ large around Iranian due process."

Trudeau pointed to a press conference Clinton gave in July 2010 in an effort to downplay the revelations contained in her private emails.

In those remarks, Clinton had compared Amiri's ability to leave the U.S. of "his own free will" with Iran's refusal to release Americans in its custody. At no point did she reference the scientist's work with the U.S. government.

McInnis said the need often arises for senior officials to talk immediately about sensitive issues when they don't have access to classified communications, forcing them to "talk around" as Clinton did by not mentioning specifics or names. Still, he said Clinton's behavior was "way beyond" the norm.

"Obviously, how Secretary Clinton was using and securing her emails, as we all know, was really inappropriate and quite dangerous. But I think almost anyone in the government recognizes there's a certain level of this challenge to be able to do your job," he said.

Chris Harmer, an analyst with the Institute for the Study of War, said that any disclosure of classified information puts current missions and future operations at risk.

"Failure to adequately safeguard current information makes it less likely that U.S. personnel or allies will put themselves at risk when U.S. leaders fail to safeguard potentially life threatening information," he said.

While it could chill someone's enthusiasm to work with the U.S. intelligence community, McInnis said that most intelligence today comes from the National Security Administration and allies, not from human intelligence.

"It's important, but U.S. national security is not going to fall apart if it becomes marginally more difficult," he said.

Edward MacMahon Jr., a national security attorney who defended CIA operative Jeffrey Sterling in a high-profile case over a leak to the New York Times, said intelligence officials often line up to argue against leaks that "chill" intelligence-gathering efforts.

"In leak prosecutions, the government alway presents this portrayal of a terrible situation in which leaks impact national security," MacMahon said.

However, MacMahon, who said he had not read the Clinton emails in question, did not believe the administration would condemn the potential exposure of Amiri.

"I doubt the government even responds," he said.

MacMahon said he did not expect to see any legal action because there is no case pending before the government in which the Amiri emails could play a role.

"I've said for a year they're not going to do anything to her," MacMahon said of Clinton's improper handling of classified information.

Amiri's case is not the first time Clinton has had to wonder about the potential impact on the intelligence community from a leak of sensitive information. Her team scrambled to deal with the fallout from a massive leak of diplomatic cables in late 2010 after the records revealed internal conversations about world leaders and international operations. The State Department set up a working group to discuss the rollout of the more than 250,000 documents, some of them classified, amid concerns that the leak could harm U.S. relations.

At the time, security experts and lawmakers worried that the cables, which were obtained and published by WikiLeaks, would harm diplomatic relations given the disclosure of conversations that were never meant to be seen by the public.

Clinton condemned the exposure of U.S. personnel in November 2010, arguing the leak could pose new risks to American officials.

"It puts people's lives in danger, threatens our national security and undermines our efforts to work with other countries to solve shared problems," she said at the time.

In preparing a "moral argument" against the publication of the cables by WikiLeaks, Daniel Baer, a high-ranking State Department official, described the danger involved with revealing individuals' activities in an email that ended up in Clinton's inbox.

"We regret the embarrassment this has caused with some of our partners," Baer wrote to Jake Sullivan, a top Clinton aide, in December 2010. "We deplore the risk it has imposed on innocent people on the front lines of struggles against corruption or rights abuses around the world."

Sullivan later passed the message along to Clinton.

The warning echoed some of the fears expressed by critics of Clinton's private email use after roughly 30,000 of her emails, made public through open records litigation, unveiled the sensitive nature of discussions that took place on her unsecured server.