As the United Nations condemned any takeover by force and the West African region's economic bloc threatened reprisals, the elite army unit's head, Mamady Doumbouya, said "poverty and endemic corruption" had driven his forces to remove President Alpha Conde from office.
"We have dissolved government and institutions," Doumbouya - a former French foreign legionnaire - said on state television, draped in Guinea's national flag and surrounded by eight other armed soldiers.
"We are going to rewrite a constitution together."
Gunfire erupted near the presidential palace in the capital, Conakry, on Sunday morning. Hours later, videos shared on social media, which Reuters could not immediately authenticate, showed Conde in a room surrounded by army special forces.
The US State Department issued a statement headed, "On the military seizure of power in Guinea," and said: "The United States condemns today's events in Conakry."
It said violence and any extra-constitutional measures would only erode Guinea's prospects for peace, stability and prosperity, and added: "These actions could limit the ability of the United States and Guinea's other international partners to support the country as it navigates a path toward national unity and a brighter future for the Guinean people."
Military sources said the president was taken to an undisclosed location and that the forces commanded by Doumbouya - whom one of the sources, a close colleague, described as calm and reserved by nature - had made several other arrests.
They included senior government officials, the sources said.
The junta that appreared to have seized power later said that Conde was not harmed, his wellbeing was guaranteed and he was being given access to his doctors.
Outgoing ministers and heads of institutions were invited to a meeting on Monday morning in parliament, they said in a statement read on the state broadcaster.
"Any failure to attend will be considered as a rebellion against the CNRD," the group said referring to its chosen name, the National Rally and Development Committee (CNRD).
Guinea's main opposition leader, Cellou Dalein Diallo, denied rumours that he was among those detained.
TAXES AND PROTESTS
Conde won a third term in October after changing the constitution to allow him to stand again, triggering violent protests from the opposition.
In recent weeks the government has sharply increased taxes to replenish state coffers and raised the price of fuel by 20%, causing widespread frustration.
By Sunday evening it was not clear if Doumbouya had taken full control, the defence ministry having issued a statement saying an attack on the presidential palace had been repelled.
But United Nations Secretary General Antonio Guterres said he strongly condemned "any takeover of the government by force" and called for Conde's immediate release.
The Economic Community of West African States (ECOWAS) threatened to impose sanctions after what its chairman, Ghana's President Nana Akufo-Addo, called an attempted coup.
The African Union said it would meet urgently and take "appropriate measures" while the foreign ministry in Nigeria, the region's dominant power, called for a return to constitutional order.
Videos shared on social media had earlier shown military vehicles patrolling Conakry, and one military source said the only bridge connecting the mainland to the Kaloum neighbourhood, where the palace and most government ministries are located, had been sealed off.
