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By Abigail Williams and Phil Helsel

Some of the billions of sanctions relief Iran will now reap could go to groups labeled terrorist organizations, Secretary of State John Kerry said Thursday.

Iran will receive approximately $55 billion after debts following the implementation of an internationally brokered nuclear agreement, Kerry said. On Saturday, the U.N. nuclear agency said it confirmed the country had complied with the deal’s terms.

"I think that some of it will end up in the hands of the IRGC [Islamic Revolutionary Guard Corps] or of other entities, some of which are labeled terrorists," Kerry said in an interview on CNBC. "To some degree, I'm not going to sit here and tell you that every component of that can be prevented."

"But I can tell you this: right now, we are not seeing the early delivery of funds going to that kind of endeavor at this point in time," Kerry said. "I'm sure at some point some of it will, but that has never made the difference in what is happening there."

Related: U.S. Marine Freed By Iran Heads Home to Michigan

Iran was labeled a state sponsor of terrorism in 1982. The Islamic Revolutionary Guard Corps-Qods Force "is the regime’s primary mechanism for cultivating and supporting terrorists abroad," according to a 2014 State Department report on state sponsors of terrorism.

Kerry said in an interview later Thursday that "Now, if we catch them funding terrorism, they’re going to have a problem with the United States Congress and with other people, obviously."

Kerry told CNBC that Iran spends $15 billion annually on its military, compared to the $80 billion spent each year by U.S. ally Saudi Arabia, and the $130 billion spent on defense by the Gulf state community.

"So it’s so incredibly disproportionate that I believe that working with our Gulf state partners — which we are going to do and which we are upgrading — we have the ability to guarantee that they will be secure, that we will stand by them even as we look for this potential of a shift in behavior," Kerry said.

It had been reported that Iran stood to gain $100 billion from the implementation of the nuclear agreement, in which international sanctions were to be lifted in exchange for Iran rolling back its nuclear program.

But the Treasury Department and an analysis by the intelligence community estimates Iran would only receive $55 billion "because a large chunk of it is already committed to China, to other countries, through loans and long term commitments that have been made," Kerry said in the interview.

Israeli Prime Minister Benjamin Netanyahu has criticized the nuclear agreement, and on Sunday he warned that "Iran has not relinquished its aspiration to obtain nuclear weapons."

Related: Obama Hails Iran Nuke Deal, Prisoner Release

Kerry told CNBC he met with Netanyahu Thursday and "of course we have a different opinion on this, and I respect completely Israel’s perception of the threat that Israel faces."

"I think there is still a skepticism on the part of some," Kerry said. "We acknowledge that, but we have the strongest security relationship with Israel on a day to day basis that has ever existed and I believe Israel will tell you that."

"Our day to day work with Israel is extraordinary and with other countries in the region," Kerry said.

Also Thursday, a U.S. Marine who was one of four Americans held by Iran who were freed in a prisoner exchange also announced Saturday returned to Michigan. U.S. officials have said that agreement was not directly linked to the nuclear deal.

A fifth American held in Iran was also freed Saturday, but his family has said he was released separately from the agreement that led to the release of the other four U.S. citizens, which included jailed Washington Post reporter Jason Rezaian.