Qureshi said, Pakistan's nuclear programme was not safe under President Asif Ali Zardari's leadership. The ex-PPP leader has recently parted company with the ruling party and announced joining Imran Khan's Pakistan Tehrik-e-Insaf party.
The former Zardari ally, made these remarks at a public rally at Ghotki in Sindh where he announced joining hands with the cricketer-turned politician. He is the highest ranking Pakistani politician to comment that the country's nuclear weapons were not safe.
His remarks come on the heels of warnings by Western experts that Islamabad's nukes could fall into the hands of Taliban terrorists.
Though Qureshi did not give details of how Pakistan's nukes were in danger but promised to talk about this in detail at the next public gathering in Karachi.
He said, he had been foreign minister and thus understood the issue well and knew the pressures and stresses Pakistan was facing over its nuclear programme. He also came down hard on the government's alliance with the US as well as US policies towards Pakistan.
Reacting angrily to Qureshi's remarks, the Pakistan government rejected his contentions as it declared there would be no compromise on a programme which is an integral to the country's defence.
Foreign Office spokesperson Tehmina Janjua said the "insinuations" made against the President were "baseless and strongly refuted".
"Our policy of maintaining credible minimum deterrence will be maintained. Under no circumstances can this national programme, which is integral to Pakistan's defence, be compromised," Janjua said.
The government, armed forces and people of Pakistan are "absolutely committed to this objective", she said.
Under the 18th constitutional amendment, all powers related to the atomic programme and nuclear arsenal were transferred to parliament and the "executive authority is vested fully with the Prime Minister", Janjua said.
In line with the amendments, the National Command Authority – which consists of the Ministers of Defence, Foreign Affairs, Interior and Finance, the Chairman of the Joint Chiefs of Staff Committee and the three service chiefs – is now headed by the Prime Minister.
The Strategic Plans Division of the National Command Authority is headed by a Director General who also serves as Secretary of the NCA.
Besides the NCA and SPD, there is the Strategic Forces Command and these "well-established institutional mechanisms are responsible for managing Pakistan"s strategic assets and programmes", Janjua said.
"We have effective custodial controls", Janjua said, adding that Pakistan is a responsible nuclear weapon state.
The NCA meets frequently to review all matters related to strategic programmes and to provide direction for upgrading these programmes to suit Pakistan"s defence requirements, she said.