Former nuclear inspectors and experts say the practice is unusual and a possible cause for concern, but whether it's ultimately problematic depends on many of the specifics of Iran's role in the inspection process.
Republicans have already seized on the arrangement as a fresh argument in opposing the deal ahead of a September vote on the agreement. The deal's backers have been concerned that a 60-day congressional review period -- about half of which has elapsed -- could be used to gin up opposition and that bad press could throw a wrench in approval of the deal.
The draft International Atomic Energy Agency arrangement has been the most dramatic international development to shake the debate around the deal since it was signed in mid-July. However, the Democrats needed to sustain Obama's promised veto of any rejection of the deal are continuing to line up behind the White House.
The Obama administration has acknowledged that Iranians would likely be involved in inspections of the Parchin military site -- which the West has widely suspected of being the site of past illicit nuclear activity -- under a draft agreement between the Iranians and the U.N.'s nuclear watchdog, the IAEA, which handles the inspections.
A senior administration official told CNN that while Iranians may be collecting the samples at Parchin, individuals from other countries would be involved in analyzing them.
It also seems likely that IAEA staff would either be present or watching via video camera and directing the Iranians when they take samples from the site.
The agreement governing the inspection of Parchin is separate from the wide-ranging inspections regime the IAEA will impose on other Iranian sites under the deal. Those inspections focus on ongoing nuclear work, whereas the investigation of Parchin is into past activities.
David Albright, an analyst who participated in nuclear inspections in Iraq, said "it is not customary at all" for the IAEA to not collect its own samples, and said if the IAEA can't visit Parchin personally to look for nooks and crannies it may want to sample, it would need robust video connections to adequately monitor the process.
"It's really not normal, and you have to worry that this would set a bad precedent in the Iran context and in the context of other countries," said Albright, president of the Institute for Science and International Security. "I don't know why they accepted it. I think the IAEA is probably getting a little desperate to settle this."
Harvard senior fellow and former IAEA deputy director general Olli Heinonen agreed the report was concerning.
"It is very unusual," he said. "I find it really hard to understand why you would let someone else take the samples and only see through the camera."
Both men, however, noted that it was important how the unfolding inspections were actually handled and the degree to which the reports about the secret draft agreement, first publicized by The Associated Press, were accurate and borne out.
"I think how this is settled could very well determine if this deal is ever implemented," Albright said, noting that it could be a moment for greater cooperation with Iran or the equivalent of a door slamming shut. "This deal can only work if it can be verified, and it can only be verified if the inspectors have access to the suspect nuclear sites."
The IAEA denied Thursday that it has made a deal with Iran giving it responsibility over inspecting Parchin.
IAEA Director General Yukiya Amano said in a statement he was "disturbed" by the suggestion, and said the confidential agreement is "technically sound and consistent with our long-established practices."
Tariq Rauf, former head of the IAEA's Verification and Security Policy Coordination Office, said having some involvement of Iranians in the inspections would be unusual but not unprecedented.
Rauf, now with the Stockholm International Peace Research Institute, said that because Parchin isn't a declared nuclear facility but rather a military site -- which countries are typically reluctant to have foreigners explore -- it would fall under the IAEA's "managed access" procedures.
Those procedures would allow Iranians to do the actual sampling of the grounds, but they would be under supervision of IAEA officials and would be using IAEA-provided equipment.
"It's not that the Iranians are going to disappear into a room and then reappear and say, 'OK, here are the swipes.' No one would ever agree to that," he said.
Rauf, who was part of a group of nuclear experts who wrote a letter supporting the Iran deal, said it would be "absolutely inconceivable" that the IAEA would have made any agreement with Iran that would impugn its credibility, which is on the line.
Rauf said that as long as there was IAEA supervision and equipment, the Iranian involvement was "not terribly concerning at all."
He charged that the leak of the draft document to AP was "a ploy by opponents of the agreement to cry or get critics in Washington to oppose it."
Critics of the deal certainly have been quick to use the issue to increase their attacks on the deal.
Freshman Sen. Tom Cotton, R-Arkansas, who in the spring penned a controversial letter opposing the Iran deal, said in a statement that the Parchin arrangement was "akin to allowing an NFL player to submit their own samples for drug testing." He continued, "Entrusting Iran to verify itself turns what is a bad deal into a farcical one."
Republicans also upped their call for the administration to release all the so-called side deals the IAEA is making with Iran over its inspections, deals that are traditionally kept confidential.
"I am disappointed the White House is claiming these secret arrangements between Iran and the IAEA are nothing but routine, technical agreements when it is anything but that," Senate Foreign Relations Committee Chairman Bob Corker, R-Tennessee, said in a statement.
"It is clear Iran out-negotiated the United States and other world powers and pushed the IAEA to commit to an incredibly unorthodox inspections process that will set a terrible precedent for the future."
Their arguments may be having an effect: A CNN/ORC Poll released Thursday found opposition to the Iran deal is up 4 points among Americans, to 56%.
But momentum also seems to be building among Democrats in Congress for supporting the deal, and some dismissed the flap around the Parchin inspections after the arrangement was made public.
Washington Rep. Adam Smith, the top Democrat on the House Armed Services Committee, told CNN's Wolf Blitzer on Thursday that Congress had been briefed on this part of the deal, and it is not cause for concern.
"I don't think it is anywhere near as alarming as it's being presented," Smith said. "It's a matter of taking samples. And the Iranians want to take the samples themselves while the IAEA monitors them taking those samples. That's it."
Smith, who said he is still deciding whether to back the deal but is leaning toward it, said his understanding is the IAEA will be able to direct Iranians about where to take the samples.
"I think this is a small issue that's being blown out of proportion by those who oppose the deal for a variety of reasons," Smith said.
Obama picked up three more Democrats in the Senate on Thursday: Sens. Claire McCaskill of Missouri, Joe Donnelly of Indiana and Ed Markey of Massachusetts. So far, 23 of the 34 Senate Democrats Obama needs to help him sustain a veto on any congressional measure of disapproval have said they will stand with him. Only two have come out against the deal.
The White House pointed to the three latest supporters as evidence for their confidence the deal will survive.
"If Republicans can't get conservative red-state Democrats with them, then that should say a lot," an administration official said, referring to Donnelly and McCaskill.
Outside groups also ramped up their action on the deal. Left-allied MoveOn sent an email to its supporters from Ben Cohen and Jerry Greenfield, founders of the eponymous ice cream company, asking them to pledge to withhold money from Democrats opposing the deal. Americans United for Change on Thursday also unveiled a TV ad campaign in support of the deal. On the other side, Citizens for a Nuclear Free Iran went up with its newest national TV ad as part of a $20 million campaign opposing the deal.