People will have to decide whether they want "elected people or a dictatorship", he added.
"I want to make it clear today that there are intrigues and conspiracies going on and the conspiracy is to pack up the elected government," Prime Minister Gilani said while addressing a function organised to commemorate the birth anniversary of Pakistan's founder Muhammad Ali Jinnah.
"I want to tell them that whether we are in government or opposition or among the people, we will fight for the rights of the people of Pakistan," he said without giving details of who was behind the conspiracies against his government.
The premier made a veiled reference to the differences between his government and the army, saying "no institution can be a state within a state".
He added: "Nobody can say they are not under the government. Every institution of this country, including the Ministry of Defence, is under the Prime Minister.
"There should be no ambiguity that anybody can claim that I am independent...If any individual thinks they are not under the government, they are mistaken.
"They are under the government and will remain under the government because we are the elected, chosen representatives of the people of Pakistan."
Gilani said the people have to decide whether they want "elected people or a dictatorship".
Prime Minister's unusual remarks came in the backdrop of tensions between the civilian government and the powerful military over the memogate scandal.
The army and ISI have urged the Supreme Court to conduct a probe into the alleged memo made public by Pakistani-American businessman Mansoor Ijaz that had sought US help to prevent a feared coup in Pakistan after the killing of Osama bin Laden in May.
However, the government has challenged the apex court's jurisdiction to hear a batch of petitions seeking a probe into the memogate scandal, saying the matter is already being investigated by a parliamentary panel.
Meanwhile, in another twist in the memogate case, the Defence Ministry yesterday informed the apex court in an affidavit that it had "no operational control" over the military or the ISI.
The ministry stated it was not in a position to confirm or deny the stand taken by the military and ISI on the memo issue.
During his address today, Gilani said his government had the "highest regard and respect for the army" because it had stood up against terrorism and extremists, but made it clear that no institution could function without the support of the people. Gilani said he had worked for public "ownership" of military operations by taking "responsibility for all military actions in country".
He further said: "No military can fight against anybody without the support of the masses. If there is no support, no war can be won."
At the same time, he appeared to hold out an olive branch to the army by saying: "My military is disciplined and they follow the constitution of Pakistan". Pakistan has been ruled by the military for almost half of its history and no elected leader has been able to complete his full term.