Siniora said on Saturday: "I call on it [the army] once again to impose security in all areas, deter the gunmen and immediately remove them from the street ...to restore normal life."
He said the Lebanese government could no longer accept Hezbollah freely holding onto its arms and said its takeover of west Beirut was a "poisonous sting".
Siniora, in his televised speech from the parliament palace in Beirut, said the government would not bow to force but would seek "dialogue through government institutions - not outside this, or through violence" but he added the "status quo" was "no longer acceptable".
He called on all Lebanese people to observe a minute's silence on Sunday to commemorate those killed in the clashes over the last four days.
'No status quo'
Rula Amin, Al Jazeera's correspondent in Beirut, said: "Siniora made an appeal when he said that the status quo that Hezbollah has enjoyed so far is not acceptable any more.
"These are very uncompromising words.
"These words Hassan Nasrallah, the leader of Hezbollah, is not going to be happy to hear because he had already made it clear that no one is to target the Hezbollah weapons, that is an issue outside discussions."
She said that Siniora had described Beirut as being "occupied" and "besieged" - strong words that would appeal not only to Lebanese inside and outside the country but also to the mostly Sunni population in the Arab world.
"He is trying to indicate that Shias were occupying the Sunni capital. What he is trying to do is trying to win the public relations campaign. He wants to put more pressure on Hezbollah," she said.
Hisham Jaber, a former Lebanese army general, told Al Jazeera: "For Hezbollah to give the government its weapons is a joke - the opposition does not trust this government."
He said: "the army would risk being divided and they are not prepared to defend any government. The army is not supposed to protect the government".
Lebanon's governing coalition on Friday described Hezbollah's takeover of west Beirut as an attempt to bring Syria back into the country and serve Iran's interests.
Siniora's speech came shortly after at least six people were reported to have been killed after unidentified armed men opened fire on a funeral procession for a pro-government supporter in Beirut.
The attack on Saturday took place after people had ventured out in small numbers to streets of the Lebanese capital held by both Lebanese troops and groups of opposition armed men.