Netanyahu's complaint came Sunday, a day after key world powers met with Iran and announced that the next meeting would take place in late May.
"My initial impression is that Iran has been given a freebie," Netanyahu said. "It has got five weeks to continue enrichment without any limitation, any inhibition."
Obama took issue with the complaint.
"Now, the clock is ticking. And I've been very clear to Iran and to our negotiating partners that we're not going to have these talks just drag out in a stalling process," he said Sunday in Cartagena, Colombia, at the Summit of the Americas. "But so far, at least, we haven't given away anything -- other than the opportunity for us to negotiate and see if Iran comes to the table in good faith.
"And the notion that somehow we've given something away or a 'freebie' would indicate that Iran has gotten something. In fact, they've got some of the toughest sanctions that they're going to be facing coming up in just a few months if they don't take advantage of these talks. I hope they do."
Saturday's talks with Iran involved the five permanent members of the United Nations Security Council -- the United States, France, Russia, China, and Britain -- as well as Germany, referred to as the P5+1.
The next set of talks was scheduled for May 23 in Baghdad.
Netanyahu said Iran should "take immediate steps to stop all enrichment, take out all enrichment material and dismantle the nuclear facility in Qom" and said the Islamic republic "must not have the opportunity to develop atomic bombs."
Iran insists that its nuclear program is for energy purposes only. U.N. and Western leaders suspect it of having military aims, including a possible nuclear weapon.
Last month, the International Atomic Energy Agency, the U.N. nuclear watchdog, noted what it called a sharp and troubling increase in Iran's uranium enrichment capabilities.
On state-run news agency IRNA, Iran described Saturday's talks in positive terms and said its right to a peaceful nuclear program was supported.
"Iran's top nuclear negotiator, Saeed Jalili, said after the Istanbul meeting that talking about suspending or halting uranium enrichment was an old issue now out-of-date," IRNA reported.
European Union foreign policy chief Catherine Ashton said after the talks, "We have agreed that the Non-Proliferation Treaty forms a key basis for what must be serious engagement to ensure all the obligations under the treaty are met by Iran while fully respecting Iran's right to the peaceful use of nuclear energy."