"Brigadier-General Wafiq Shqeir will remain in his post until appropriate procedural measures have been taken after a probe," the statement said.
As for Hezbollah's communications network, the army said the issue would be handled by its Signal Corps.
The network was previously deemed "illegal" by the government.
Agencies said on Saturday that opposition fighters who had routed supporters of the governing March 14 coalition the previous day, were seen driving out of Beirut's seaside front and other areas.
In their place, Lebanese soldiers were seen patrolling the streets.
Mustafa Allouch, a member of parliament, said Hezbollah's decision to withdraw its fighters is a good start.
"What is important for us is to stop the bloodshed that Hezbollah has started," he said.
"Our priority now is to stop the killing, and to withdraw all the militias off the streets."
The developments in Beirut came as reports from northern Lebanon spoke of the deaths of at least 14 people in clashes.
According to a Lebanese security official, fighting in the town of Halba in the Akkar region pitted a party allied with the opposition against government supporters.
"The headquarters of the Syrian Social National Party (SSNP) in Halba fell to the Future Movement forces," the official said, referring to the party of Saad Hariri, the leader of the March 14 camp and son of Rafiq al-Hariri, the assassinated former Lebanese prime minister.
The official said that seven people were found dead inside.
Dozens of people have been killed since Wednesday in the worst clashes in Lebanon since the 1975-1990 civil war.
Earlier on Saturday, Siniora, speaking from the parliament palace in his first public response to opposition fighters' takeover of west Beirut,
appealed to the army to impose security throughout the country.
He called on the military to remove armed men from the streets and restore law and order, even as he accused Hezbollah of carrying out an "armed coup" against Lebanon.
Siniora said the Lebanese government could no longer accept Hezbollah freely holding on to its arms and said its takeover of west Beirut was a "poisonous sting".
He said the government would not bow to force but would seek "dialogue through government institutions - not outside this, or through violence".
However, he said the "status quo" was "no longer acceptable".
Siniora also 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.
The governing coalition on Friday described the takeover of west Beirut by opposition fighters as an attempt to bring Syria back into the country and serve Iran's interests.
Hassan Khalil, a spokesman for Amal, a Hezbollah ally, said: "The government has to first show the courage to implement the army's demands to revoke the wrong decisions."
He said the opposition would continue its civil disobedience campaign against the government.
'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."
|The army previously said that|
continued conflict threatens its unity [Reuters]
Amin noted that Siniora described Beirut's condition as "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.
Commenting on Siniora's speech, 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."
Jaber 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".
Siniora's speech came shortly after at least six people were reported to have been killed when unidentified armed men opened fire on a funeral procession for a pro-government supporter in Beirut on Saturday.
The attack took place after people had ventured out in small numbers to streets, occupied by both Lebanese troops and groups of opposition armed men.
Witnesses in the area said a car drove close by and opened fire on about 200 mourners at Tarik Jadideh cemetery near an area controlled by opposition forces.
Later on Saturday, Hezbollah blamed Walid Jumblatt, a senior figure in the March 14 camp and leader of the Druze community, for the deaths of at least two of its members in Aley, east of Beirut.
Jumblatt admitted there had been "an unfortunate incident" in the predominantly Druze and Christian town, saying: "Three people were killed. Two bodies were found and turned over to the army."
He did not openly admit his supporters were responsible, but said if unconfirmed reports that the victims had been tortured proved true, he would "personally take responsiblity for it".
Source: Al Jazeera and agencies