The two issues “unfortunately, are still in the category of unresolved issues," Russian Deputy Foreign Minister Sergei Ryabkov said on Wednesday.
"I do not want to single out any of them with respect to other aspects not because it is hard for us to determine what is at the center and what remains on the side, but because we have been dealing with this as a package for a long time and the internal balances between the different components of the deal are very sensitive," Ryabkov stressed.
He also said that a deal between Iran and the five permanent members of the United Nations Security Council -- Russia, China, France, Britain and the United States -- plus Germany will help security in the region.
"Despite the attempts of some circles in the international community to question the appropriateness of this agreement…we believe that the outcome that we currently foresee for these negotiation efforts would definitely strengthen global and regional security," Ryabkov said.
Nuclear negotiators from Iran and the P5+1 are currently in the Swiss city of Geneva discussing Iran nuclear program three weeks after Tehran and the six countries failed to reach a final agreement by a November 24 deadline.
Despite making progress, Iran and the P5+1 group failed to clinch a final nuclear deal during their previous talks in the Austrian capital of Vienna.
However, the two sides agreed to extend their discussions for seven more months until July 1, 2015. They also agreed that the interim deal they had signed in Geneva last November remain in place during the negotiations.
The Arak reactor, which uses natural uranium to produce radio medicines, is planned to gradually replace the Tehran Research Reactor, which produces medical radioisotopes for cancer patients.
In May, Iran said the facility will remain a heavy water reactor, but will be redesigned to produce less plutonium.
The US and its European allies have imposed sanctions against Iran under the allegation that the Islamic Republic pursues non-civilian objectives in its nuclear work. Iran denies the accusation.