Egyptian air force fighter planes buzzed low over Cairo, helicopters hovered above and extra troop trucks appeared in a central square where protesters were demanding an end to President Hosni Mubarak's rule.
State television said that a curfew has been imposed in the capital and the military urged the protesters to go home.
But the thousands of protesters in Tahrir Square chose to stay on Sunday.
The show of defiance came as Egypt entered another turbulent day following a night of deadly unrest, when looters roamed the streets in the absence of police.
Opposition groups in the country have called for national unity, and Mohamed Elbaradei, a leading opposition figure, has arrived at Tahrir Square to join the protests.
The National Coalition for Change, which groups several opposition movements including the Muslim Brotherhood, appointed ElBaradei with negotiating with Mubarak's government.
As the protests continue, security is said to be deteriorating and reports have emerged of several prisons across the country being attacked and of fresh protests being staged in cities like Alexandria and Suez.
Thirty-four leaders from the Muslim Brotherhood were freed from the Wadi Natroun jail after guards abandoned their posts.
The protesters in Cairo, joined by hundreds of judges, had collected again in Tahrir Square afternoon to demand the resignation of Hosni Mubarak, the Egyptian president.
Al Jazeera's correspondent, reporting from the scene, said that demonstrators confronted a fire truck, at which point army troops fired into the air in a bid to disperse them.
He said the protesters did not move back, and a tank commander then ordered the fire truck to leave. When the truck moved away from the square, the thousands of protesters erupted into applause and climbed onto the tank in celebration, hugging soldiers.
Main roads in Cairo have been blocked by military tanks and armored personnel carriers, and large numbers of army personnel have been seen in other cities as well.
Reporting from Cairo earlier on Sunday, Al Jazeera's Dan Nolan said it was a "long way from business as usual" in the Egyptian capital on the first working day since protests peaked on Friday.
He said that extra military roadblocks had been set up in an apparent attempt to divert traffic away from Tahrir Square, which has been a focal point for demonstrators.
"It's still a very tense scene to have so much military in the capital city of the country."
Earlier in the morning, Al Jazeera's Jane Dutton, also in Cairo, reported that the city appeared deserted in the early hours.
"The streets are very dirty, there is debris everywhere. The police have just disappeared. Any security at this stage is in the hands of the army."
Al Jazeera's correspondents in the port city of Alexandria have also said that anti-government protests have begun there, with hundreds of people on the streets.
The air force in Cairo has been attempting to disperse protesters, with fighter planes flying low over Tahrir Square on Sunday.
Al Jazeera correspondents say the noise from the planes was deafening and that the planes repeatedly flew over the crowds.
The security situation in the capital has prompted the country's interior minister to hold meetings with top officials on Sunday.
Habib al Adli met Mohamed Hussein Tantawi, the defence minister, and vice president Omar Soliman, state television reported.
As the police withdrew from streets across Egypt, Adli has been the target of growing criticism by the protesters who have called on him to resign.
The absence of police has given looters a free rein, forcing ordinary citizens to set up neighborhood patrols.
According to Dina Magdi, an eyewitness, unidentified men on Sunday morning came out of the interior ministry compound in a car and dumped a body on a street. They then opened fire on people present in the area and fled. There were no immediate reports of casualties in that attack.
Al Jazeera's sources have indicated that the military has now also been deployed to the resort town of Sharm el Shaikh.
Sherine Tadros, Al Jazeera's correspondent in the city of Suez, said the city had witnessed a "completely chaotic night", but that the streets were quiet as day broke.
She reported that in the absence of police and military, people were "tak[ing] the law into their own hands", using "clubs, batons, sticks, machetes [and] knives" to protect their property.
"People are trying to get back to normal, but of course this is anything but," she said, adding that as the day wore on, the military had set up several checkposts in an attempt to "show people that they are here and ... will provide some kind of security".
Rawya Rageh, our correspondent in Alexandria, reported similar scenes, saying that people were particularly concerned about their personal safety and that of their property.
She reported that the military in Alexandria was not focusing on protesters, attempting instead to prevent any further damage or theft of property.
Anti-Mubarak protests have engulfed Middle East's most populous nation since last Tuesday. More than 150 people have been killed in the unrest.
On Saturday, an embattled Mubarak sacked his cabinet and appointed a vice-president and a new prime minister. But the move has failed to douse anger on the streets
Dutton said that protesters are unlikely to stop demonstrating, as they "want one thing, and one thing only: they want the leadership to go".
As international powers express concern regarding events in Egypt, the US state department has reduced its diplomatic presence in Egypt, saying it had authorized the voluntary departure of dependents of diplomats and non-essential workers.