"I understand people have anxieties about this deal," he told MSNBC's "Morning Joe." "It is far from perfect, but it is the best thing we have at the moment."
He added: "It has stopped the Iranians getting a nuclear weapon; we have to ask ourselves, 'How else would we do that?'"
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The 2015 deal, formally known as the Joint Comprehensive Plan of Action, offered Tehran billions of dollars in relief from sanctions in exchange for its agreement to curb its nuclear program.
Trump wants to ditch the Obama-era accord, which expires in 2025, and says he will refuse to extend U.S. sanctions relief for Iran unless it is renegotiated.
Britain, France and Germany believe the deal is worth saving because it gets rid of 95 percent of Iran’s enriched uranium and allows U.N. inspections with no advance notice.
"We can meet the president's challenge without throwing away the heart of the deal," Johnson told MSNBC's Joe Scarborough.
In an opinion article for Monday’s New York Times, Johnson warned Trump that abandoning the deal would end the international inspections.
“Now that these handcuffs are in place, I see no possible advantage in casting them aside,” Johnson wrote. “At this delicate juncture, it would be a mistake to walk away from the nuclear agreement and remove the restraints that it places on Iran.”
He added: "I believe that keeping the deal’s constraints on Iran’s nuclear program will also help counter Tehran’s aggressive regional behavior. I am sure of one thing: Every available alternative is worse. The wisest course would be to improve the handcuffs rather than break them.”
Israel has long opposed the pact, saying it hasn't curbed Iran's wider aggression, such as its support for Hezbollah — a powerful Lebanese militia and political group — and its role in conflicts in Syria, Yemen, Iraq and Bahrain.
In his previous role as CIA director, Pompeo consistently portrayed Iran as the focus of evil in the Middle East and a worldwide threat. However, State Department official Brian Hook has been working on a compromise that would see the U.S. remain in the nuclear deal while extending its limitations to cover Iran’s missiles.
Iran's President Hassan Rouhani said Sunday he would respond to any move to end the deal and warned that the United States would regret such a decision to abandon the pact.
"America is making a mistake if it leaves the nuclear accord," he said.