Troops were also seen attacking people, including journalists, with batons as they advanced towards small groups of protesters gathered at what had become known as the "GotaGoGama (village)".
At least 50 protesters were injured, the organisers said. Hospital sources said two were hospitalised.
The head of the influential Bar Association of Sri Lanka, Saliya Peiris, condemned the military action and warned it would hurt the new government's international image.
"Unnecessary use of brute force will not help this country and its international image," Peiris said in a brief statement. He said several people, including a lawyer, had been detained by security forces.
"The various steps being taken including declaring an emergency and calling out the troops, raises serious concerns this government is taking on fundamental rights and the rule of law in Sri Lanka," said Bhavani Fonseka, a senior researcher at Colombo-based think tank Center for Policy Alternatives.
"The excessive force and the violence used to remove protesters is a marked difference from what Sri Lanka needs right now, especially when the protesters had already said they will vacate the premises," he added.
The military used loud-hailers as they ordered a few hundred men and women camping overnight to pull back and confine themselves to a designated protest site near the secretariat.
Police cordoned off the main roads leading to the area to prevent more people from joining the protesters.
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