The offer came a day after a report by a Harvard non-proliferation expert was released, which said that country's nuclear arsenal faces "immense" threats and is the world's least secure from theft or attack.
Speaking to Al Jazeera, however, Masood Khan, Pakistan's chief negotiator on nuclear affairs, rebutted the claim, saying the country's small but growing weapons stockpile was "completely safe".
"... I think we can be very confident our programme is secure and safe"
Masood Khan, Pakistan's chief nuclear negotiator
"One of the reasons is, all our programmes are in the public sector, so we have direct control over all fissile materials and facilities, and we have a very elaborate command and control system, we have a regulatory regime [and] we have export laws," he said.
"We are also co-ordinating with the international community, so I think we can be very confident our programme is secure and safe."
Obama, hosting more than 40 countries to discuss world nuclear issues, also defended Pakistan, saying he was confident their nuclear weapons were safe, but that security could still be improved.
"I feel confident about Pakistan's security around its nuclear weapons programmes but that doesn't mean that there isn't improvement to make in all of our nuclear security programmes."
Pakistan has in the past courted controversy over its nuclear programme.
In 2004, Abdul Qadeer Khan, the country's former chief nuclear scientist, admitted to selling uranium enrichment technology to Iran, Libya and North Korea.
IAEA officials and analysts say that Khan's actions led to one of the greatest nuclear proliferation crises of the atomic age.
Pakistan has also faced criticism over instability in the country, as the conflict with pro-Taliban and al-Qaeda fighters has led to fears that nuclear material will fall into their hands.
The report, released on Monday by Matthew Bunn, a Harvard University professor, said Pakistan's nuclear stockpile "faces immense threats, both from insiders who may be corrupt or sympathetic to terrorists and from large attacks by outsiders".
Pakistan has not signed onto the 1970 nuclear Non-Proliferation Treaty.