He repeatedly criticized the Tehran government for failing to disclose all its nuclear-related activities.
Then there are research centers and military installations where the United States suspects - but cannot prove - that clandestine nuclear-related activity may be taking place.
Obama said: "This site deepens a growing concern that Iran is refusing to live up to those international responsibilities, including specifically revealing all nuclear-related activities.
None of this will guarantee Tehran's compliance with international demands to disclose all its nuclear-related activities.
Indeed, in defending Iran's decision, the letter said that the suspension of the country's nuclear-related activities under the European agreement had been "voluntary and non-legally binding."
And United States intelligence analysts acknowledge that they do not know where all of Iran's secret nuclear-related activities are situated.
Nor can inspectors rule out the possible involvement of Iran's military in nuclear-related activities.
I strongly urge the DPRK to suspend all missile and nuclear-related activity and to commit to re-engaging with the international community.
There did not appear to have been any nuclear-related activity on this stretch of desert for many years.
Meanwhile, American officials said their intelligence agencies reported no major nuclear-related activity.