Seoul, South Korea (CNN) -- The United States and its allies are working on steps to take against Iran after its apparent rejection of a nuclear deal, U.S. President Obama said Thursday.

"We have begun discussions with international partners about the importance of having consequences," Obama said. "Our expectation is that over the next several weeks, we will be developing a package of potential steps we could take that will indicate our seriousness to Iran. I continue to hold out the prospect that they may decide to walk through this door. I hope they do."

On Wednesday, Iran rejected a key plank of a deal designed to ease international fears that Tehran aims to build nuclear weapons.

Foreign Minister Manouchehr Mottaki said Iran will not send its partially enriched uranium abroad to be turned into material for medical research, but added than Tehran might allow its nuclear material to be reprocessed inside Iran, the semi-official ISNA news agency reported.

The deal hammered out in October with the help of the United Nations' nuclear watchdog agency aimed to reduce the amount of raw material Iran has to build a nuclear bomb.

Tehran denies that it wants to do so, saying its nuclear program is used for civilian and medical purposes.

The watchdog International Atomic Energy Agency said Wednesday it could not confirm or deny that Iran had rejected any part of the proposal.

U.S. State Department spokesman Ian Kelly said, "This is the IAEA's proposal, and Iran has to give their response to the IAEA, and that's what we're waiting for. That's what the IAEA is waiting for."

But, Kelly said, "until the IAEA gets the response and formally says this is ... Iran's response, I don't consider a statement to the press necessarily a response."

On October 1, the IAEA proposal "was accepted in principle by all the parties including Iran," Kelly said. "And there was also an agreement that each of the parties would provide a written response to the proposal.

"Russia, France and the United States have provided a written response," he said. "We expect Iran to provide a written response. And we expect the IAEA to pronounce on that response. So we will wait for the IAEA to make a formal response to this."

In a report published Monday, the IAEA expressed concerns about Iran's nuclear program.

The Islamic republic's disclosure of a previously secret nuclear facility near Qom raised questions about the existence of other such facilities, and its delay in acknowledging the facility "does not contribute to the building of confidence" in Tehran, the IAEA said in the report.

Tehran has not convinced the agency its nuclear program isn't military, said the report, published on the Institute for Science and International Security Web site. A source with direct knowledge of the report confirmed its authenticity to CNN.

Tehran shocked the international community in September by revealing the existence of the nuclear enrichment facility.

On Monday, Kelly said in a statement the report "underscores that Iran still refuses to comply fully with its international nuclear obligations."

IAEA inspectors visited the newly revealed facility in October, according to the report.

During a meeting in Tehran, Iranian officials told the inspectors that construction of the site had begun during late 2007, the report said, and it would not be operational until 2011.

However, the IAEA inspectors told Iran "it had acquired commercially available satellite imagery of the site indicating that there had been construction at the site between 2002 and 2004, and that construction activities were resumed in 2006 and had continued to date," the report said.

IAEA member states also allege that design work on the facility, the Fordow Fuel Enrichment Plant, began in 2006, the report said.

Iranian officials told inspectors that the nation has no other undisclosed nuclear facilities either under construction or in operation, the report said, and promised that any future facilities would be disclosed. A letter sent earlier in November asks Tehran to confirm it has not decided to construct or authorized construction of any undisclosed facility, the report said.

Iran remains bound by the terms of a 2003 agreement under which it must provide information to the IAEA regarding nuclear facilities as soon as the decision to build is made or construction is authorized.

"Even if, as stated by Iran, the decision to construct the new facility at the Fordow site was taken in the second half of 2007, Iran's failure to notify the agency of the new facility until September 2009 was inconsistent with its obligations," the IAEA said.

U.N. Secretary-General Ban Ki-moon has said that construction of the facility violates U.N. Security Council resolutions, Kelly said.

"Iran's delay in submitting such information to the agency does not contribute to the building of confidence," the report said. "While the agency has confirmed that the plant corresponds to the design information provided by Iran, Iran's explanation about the purpose of the facility and the chronology of its design and construction requires further clarification."

The agency is waiting for Iran's reply to its request to meet officials in regard to those issues and others, according to the report.

"Further analysis of the information available to the agency underscores the importance of Iran engaging with the agency in a substantive and comprehensive manner, and providing the requested access, so that the remaining outstanding issues may be resolved."

The agency encouraged IAEA member states who have provided it information on Iran to share that information with Tehran as well.