The comments follow remarks made by Russian President, Vladamir Putin, that weapons of mass destruction in the country could fall into the hands of "bandits and terrorists."
Mr Putin, in an interview with The Hindu newspaper ahead of a three-day visit to India, said Russia remained worried about the problem - despite Pakistani efforts to deal with it.
On Sunday, a Pakistani foreign ministry spokesman responded by saying Russia's own system of safeguarding its nuclear assets was a matter of serious concern to the international community.
Bilateral meeting
Islamabad also said it was concerned about the Russian foreign ministry's comments to the effect that the seizure of a Hindu temple in Indian-administered Kashmir was connected to a "terrorist infrastructure" in Pakistan.
Pakistan intends to take up the issue with the Russian authorities at a bilateral meeting of the Joint Working Group in Moscow on Monday.
But Prime Minister Vajpayee repeated the Russian president's concerns by saying: "This matter raised by President Putin must be taken seriously by the entire world."
Despite concerns, President Putin praised efforts by Pakistan and India to withdraw troops from their shared border.
He said: "I think that relaxation of tension in such an explosive and dangerous region is an act that deserves respect and we will try to support any steps taken by either country towards that objective."
President Putin is to hold talks with Indian Prime Minister Atal Behari Vajpayee and a host of cabinet ministers during his visit.
India and Russia are long-time allies and Mr Putin was last here in 2000, while Mr Vajpayee went to Moscow last year.
Both India and Pakistan have tested nuclear devices, and the two countries remain locked in a potentially deadly stand-off over the disputed territory of Kashmir.